Variant report

Variant	rs928015
Chromosome Location	chr1:92414072-92414073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1073001	0.91[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs10783071	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10783072	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10783074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs10875067	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875068	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875081	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875082	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875083	0.80[ASN][1000 genomes]
rs10875096	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875101	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11165840	0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11165842	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11165853	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165878	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165898	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165904	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040031	0.97[ASN][1000 genomes]
rs12060343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12725353	0.86[ASN][1000 genomes]
rs12732002	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733726	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12741192	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1887812	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963186	0.90[JPT][hapmap]
rs3767854	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767855	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4658118	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4658119	0.97[ASN][1000 genomes]
rs4658123	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4658281	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658283	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4658286	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61779126	0.90[ASN][1000 genomes]
rs6656733	0.80[JPT][hapmap]
rs6656817	0.94[ASN][1000 genomes]
rs6663816	0.81[JPT][hapmap]
rs6666624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677351	0.97[ASN][1000 genomes]
rs6686166	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689033	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6690705	0.83[CHB][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap]
rs6692045	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap]
rs6696267	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs6697441	0.83[CHB][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap]
rs6702511	0.94[ASN][1000 genomes]
rs7355067	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7541712	0.97[ASN][1000 genomes]
rs7551956	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7553278	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766665	0.97[ASN][1000 genomes]
rs766666	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9803619	0.94[ASN][1000 genomes]
rs9887935	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases
20	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
21	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv830581	chr1:92317207-92511175	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	nsv871415	chr1:92340684-92641607	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	esv2750842	chr1:92356781-92579675	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
26	nsv871144	chr1:92380302-92641607	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs928015	RPAP2	cis	cerebellum	SCAN
rs928015	CREG1	trans	cerebellum	SCAN
rs928015	FAM69A	cis	cerebellum	SCAN
rs928015	NPC1	trans	parietal	SCAN
rs928015	ZNF326	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92411200-92414200	Weak transcription	Placenta	Placenta
2	chr1:92412600-92414200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr1:92413000-92415400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:92413600-92414600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:92413600-92415000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr1:92413600-92415000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:92413800-92414200	Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr1:92413800-92414600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:92413800-92414800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr1:92413800-92414800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:92414000-92414200	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:92414000-92414400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:92414000-92414400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:92414000-92414600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:92414000-92414800	Enhancers	GM12878-XiMat	blood
16	chr1:92414000-92415000	Enhancers	Fetal Thymus	thymus

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