Variant report

Variant	rs2524040
Chromosome Location	chr6:31257625-31257626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2213140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243866	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524158	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2524159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524161	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2524163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853918	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2853933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:68 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
8	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
9	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
10	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
11	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
12	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
13	nsv1034391	chr6:31131121-31279595	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1025909	chr6:31131121-31354706	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
15	nsv538175	chr6:31131121-31354706	Active TSS Bivalent Enhancer Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
16	nsv1015890	chr6:31131121-31449207	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
17	nsv538176	chr6:31131121-31449207	Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
18	nsv1024887	chr6:31162849-31354706	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
19	nsv538177	chr6:31162849-31354706	Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
20	nsv1015903	chr6:31162849-31412740	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
21	nsv538178	chr6:31162849-31412740	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
22	nsv1031682	chr6:31162849-31449207	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
23	nsv538179	chr6:31162849-31449207	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
24	esv3381377	chr6:31192213-31498578	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
25	esv3340592	chr6:31192248-31498535	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
26	nsv432867	chr6:31196671-31343862	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
27	esv5999	chr6:31206410-31285897	Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
28	esv3373199	chr6:31206451-31287335	Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
29	nsv538180	chr6:31206639-31386279	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	42 gene(s)	inside rSNPs	diseases
30	nsv1029142	chr6:31206639-31449207	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
31	nsv1021052	chr6:31206639-31485736	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
32	esv6375	chr6:31210228-31287149	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
33	esv3475032	chr6:31210396-31321602	Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
34	esv3475033	chr6:31210396-31321602	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
35	esv3494518	chr6:31213606-31289031	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
36	esv3494520	chr6:31213606-31289031	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
37	esv2422229	chr6:31215949-31322934	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
38	esv3328153	chr6:31230846-31327330	Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
39	esv2503823	chr6:31233039-31319362	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
40	esv35158	chr6:31233510-31318221	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
41	esv3475034	chr6:31234427-31327274	Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
42	esv3475035	chr6:31234427-31327274	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
43	esv5788	chr6:31234471-31320006	ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
44	esv6661	chr6:31236449-31321770	Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
45	nsv601502	chr6:31237229-31298743	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
46	nsv601503	chr6:31237229-31336891	Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
47	nsv601506	chr6:31237405-31310056	Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
48	nsv601507	chr6:31237586-31339844	Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
49	esv3368459	chr6:31237898-31323062	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
50	esv6770	chr6:31238482-31323891	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2524040	HLA-C	cis	lymphoblastoid	GTEx
rs2524040	HLA-DRB5	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31257200-31257800	Enhancers	GM12878-XiMat	blood
2	chr6:31257600-31258000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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