Variant report

Variant	rs9292618
Chromosome Location	chr5:35878512-35878513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10043573	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10053847	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056484	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10058680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10059688	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10070378	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10472264	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10472989	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10472990	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1073290	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11567722	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11567738	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11567754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11567761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12520952	0.90[EUR][1000 genomes]
rs13154973	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13162685	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13167136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169780	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13169814	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13170810	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13172065	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1389834	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];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16899999	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1862632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161552	0.90[JPT][hapmap]
rs2228141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34496007	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35467464	0.90[EUR][1000 genomes]
rs35588638	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4521502	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4601063	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4869430	0.83[ASN][1000 genomes]
rs4869492	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4869674	0.84[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs6451229	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs6451234	0.85[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs6451236	0.83[ASN][1000 genomes]
rs66570838	0.90[EUR][1000 genomes]
rs6859892	0.81[ASN][1000 genomes]
rs6888699	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6891095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6892488	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6897339	0.87[CHD][hapmap]
rs7445819	0.83[ASN][1000 genomes]
rs7710177	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7718489	0.85[EUR][1000 genomes]
rs7718919	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7727750	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs969128	0.86[GIH][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9292618	BRIX1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
2	chr5:35866600-35878800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr5:35866600-35882000	Genic enhancers	Dnd41	blood
4	chr5:35867800-35879800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr5:35873200-35880200	Genic enhancers	Primary T cells from cord blood	blood
6	chr5:35873200-35880200	Genic enhancers	Thymus	Thymus
7	chr5:35873400-35880000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr5:35875400-35883200	Genic enhancers	Fetal Thymus	thymus
9	chr5:35876600-35884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:35876800-35883600	Weak transcription	Osteobl	bone
11	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:35877000-35880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:35877200-35879200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:35877400-35879800	Strong transcription	NHLF	lung
17	chr5:35877400-35883600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:35877600-35883200	Weak transcription	NHEK	skin
19	chr5:35877800-35881000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:35878000-35879200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr5:35878000-35881000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:35878000-35882000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:35878000-35882000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:35878000-35882200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:35878200-35878800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:35878200-35879000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:35878200-35879800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr5:35878200-35880000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:35878200-35883600	Weak transcription	HSMM	muscle
30	chr5:35878400-35878800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:35878400-35879000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr5:35878400-35880400	Weak transcription	Hela-S3	cervix
33	chr5:35878400-35882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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