Variant report

Variant	rs4379368
Chromosome Location	chr7:40466200-40466201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10234636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10245007	0.99[ASN][1000 genomes]
rs10250287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10256791	0.81[JPT][hapmap]
rs10951634	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs11531505	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766930	0.88[ASN][1000 genomes]
rs11772069	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs11980965	0.98[ASN][1000 genomes]
rs12234460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531683	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532479	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12533531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12538229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12670267	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12673516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs12701822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1319467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16880229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17171680	0.81[JPT][hapmap]
rs17171683	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs17171686	0.87[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs17171693	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs17171694	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs17171696	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs17171703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17171704	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17171705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17171710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2190261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3890819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4143205	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs4421260	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4434532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452702	0.85[JPT][hapmap]
rs4526265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563791	0.97[ASN][1000 genomes]
rs4612243	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4723954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59682057	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6462972	0.85[JPT][hapmap]
rs6462976	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs6945101	0.80[JPT][hapmap]
rs6965764	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs7782189	0.99[ASN][1000 genomes]
rs7807217	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs9690724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv817404	chr7:40295934-40573605	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv949540	chr7:40321357-40528147	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34484	chr7:40383159-40489083	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2757223	chr7:40384030-40497278	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2759526	chr7:40384030-40497278	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv8081	chr7:40393228-40486239	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1016800	chr7:40409214-40470294	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1015701	chr7:40409214-40474936	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv830969	chr7:40422576-40582389	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv1027075	chr7:40438478-40479723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv1026022	chr7:40440560-40479066	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
14	esv2761320	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv1032028	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv1032883	chr7:40440560-40489083	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1019992	chr7:40443653-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv1017615	chr7:40445480-40570791	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Migraine without aura	23793025	GWAS catalog
Migraine - clinic-based	23793025	GWAS catalog
Migraine	23793025	GWAS catalog

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40458400-40473200	Weak transcription	Aorta	Aorta
2	chr7:40459800-40467400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:40459800-40469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:40460000-40467400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:40464800-40466800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:40465000-40466800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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