Variant report

Variant	rs58161072
Chromosome Location	chr6:29971574-29971575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29971567-29971617	Hepatocyte	liver:	n/a
2	chr6:29971567-29971617	NHDF-neo	bronchial:	n/a
3	chr6:29971567-29971617	NT2-D1	testis:	n/a
4	chr6:29971567-29971617	HCPEpiC	choroid plexus:	n/a
5	chr6:29971567-29971617	Hela-S3	cervix:	n/a
6	chr6:29971567-29971617	GM12878	blood:	n/a
7	chr6:29971567-29971617	HCM	heart:	n/a
8	chr6:29971567-29971617	HEK293	kidney:	embryo
9	chr6:29971567-29971617	BE2_C	brain:	n/a
10	chr6:29971567-29971617	NHBE	bronchial:	n/a
11	chr6:29971567-29971617	HRPEpiC	eye:	n/a
12	chr6:29971567-29971617	NB4	blood:	n/a
13	chr6:29971567-29971617	MCF-7	breast:	n/a
14	chr6:29971567-29971617	ECC-1	luminal epithelium:	n/a
15	chr6:29971567-29971617	HUVEC	blood vessel:	n/a
16	chr6:29971567-29971617	SK-N-SH_RA	brain:	n/a
17	chr6:29971567-29971617	PFSK-1	brain:	n/a
18	chr6:29971567-29971617	A549	lung:	n/a
19	chr6:29971567-29971617	HIPEpiC	eye:	n/a
20	chr6:29971567-29971617	BJ	skin:	n/a
21	chr6:29971567-29971617	T-47D	breast:	n/a
22	chr6:29971567-29971617	AG09319	gingival:	n/a
23	chr6:29971567-29971617	GM19239	blood:	n/a
24	chr6:29971567-29971617	GM06990	blood:	n/a
25	chr6:29971567-29971617	RPTEC	kidney:	n/a
26	chr6:29971567-29971617	HCT-116	colon:	n/a
27	chr6:29971567-29971617	U87	brain:	n/a
28	chr6:29971567-29971617	HPAEpiC	pulmonary alveolar:	n/a
29	chr6:29971567-29971617	PrEC	prostate:	n/a
30	chr6:29971567-29971617	LNCaP	prostate:	n/a
31	chr6:29971567-29971617	Caco-2	colon:	n/a
32	chr6:29971567-29971617	SKMC	muscle:	n/a
33	chr6:29971567-29971617	NH-A	brain:	n/a
34	chr6:29971567-29971617	SK-N-MC	brain:	n/a
35	chr6:29971567-29971617	SAEC	small airway:	n/a
36	chr6:29971567-29971617	HRCEpiC	kidney:	n/a
37	chr6:29971567-29971617	MCF10A-Er-Src	breast:	n/a
38	chr6:29971567-29971617	HEEpiC	esophagus:	n/a
39	chr6:29971567-29971617	HCF	heart:	n/a
40	chr6:29971567-29971617	HMEC	breast:	n/a
41	chr6:29971567-29971617	AG10803	skin:	n/a
42	chr6:29971567-29971617	GM12891	blood:	n/a
43	chr6:29971567-29971617	Jurkat	blood:	n/a
44	chr6:29971567-29971617	ProgFib	skin:	n/a
45	chr6:29971567-29971617	ovcar-3	ovarian:	n/a
46	chr6:29971567-29971617	HepG2	liver:	n/a
47	chr6:29971567-29971617	AG04450	lung:	fetal
48	chr6:29971567-29971617	AoSMC	blood vessel:	n/a
49	chr6:29971567-29971617	HAEpiC	amniotic membrane:	n/a
50	chr6:29971567-29971617	GM12892	blood:	n/a

No data

Variant related genes	Relation type
HLA-J	CpG island

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10484549	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16896044	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16896923	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896970	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17179992	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17180093	1.00[AFR][1000 genomes]
rs17180107	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17180227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17180836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17186566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17187693	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17193696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17194467	1.00[AFR][1000 genomes]
rs2275854	0.84[ASN][1000 genomes]
rs2286404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2893999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3823368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3869062	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4087724	1.00[AFR][1000 genomes]
rs4087726	1.00[AFR][1000 genomes]
rs41540614	1.00[AFR][1000 genomes]
rs41545022	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs41545117	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs41547618	1.00[AFR][1000 genomes]
rs41562213	1.00[AFR][1000 genomes]
rs55664658	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55808509	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55897388	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs55901207	1.00[AFR][1000 genomes]
rs55975201	1.00[AFR][1000 genomes]
rs56052321	1.00[AFR][1000 genomes]
rs56073777	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56147022	1.00[AFR][1000 genomes]
rs56149225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56171155	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56181708	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56185319	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56232426	1.00[AFR][1000 genomes]
rs56270681	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56289102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56369124	1.00[AFR][1000 genomes]
rs56378970	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58309428	1.00[AFR][1000 genomes]
rs61180635	1.00[AFR][1000 genomes]
rs62388660	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62388661	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62388723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62388749	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388750	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388751	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388752	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388754	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388755	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388756	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62388757	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62388764	1.00[AFR][1000 genomes]
rs62388798	1.00[AFR][1000 genomes]
rs62388799	1.00[AFR][1000 genomes]
rs62388801	1.00[AFR][1000 genomes]
rs62388802	1.00[AFR][1000 genomes]
rs62390160	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390162	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390181	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62390400	1.00[AFR][1000 genomes]
rs62390401	1.00[AFR][1000 genomes]
rs62390402	1.00[AFR][1000 genomes]
rs62390510	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62390517	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62390553	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62390555	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62392214	1.00[AFR][1000 genomes]
rs62392216	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS 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 target site	16 gene(s)	inside rSNPs	diseases
10	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
13	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
14	nsv601475	chr6:29963179-29977973	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29964400-29974400	Weak transcription	Hela-S3	cervix
2	chr6:29966800-29974000	Weak transcription	Spleen	Spleen
3	chr6:29970800-29973800	Weak transcription	Ovary	ovary
4	chr6:29971000-29973800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:29971000-29974000	Weak transcription	HMEC	breast

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