Variant report

Variant	rs3851784
Chromosome Location	chr17:45040117-45040118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1047779	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052504	0.99[ASN][1000 genomes]
rs1052586	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853085	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10853087	0.99[ASN][1000 genomes]
rs11079742	0.82[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11079745	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11652318	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654971	0.99[ASN][1000 genomes]
rs11655668	0.86[JPT][hapmap]
rs11656362	1.00[ASN][1000 genomes]
rs11658276	0.97[ASN][1000 genomes]
rs11869840	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601886	0.99[ASN][1000 genomes]
rs12940071	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1618989	0.98[ASN][1000 genomes]
rs1623402	0.99[ASN][1000 genomes]
rs1662576	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662577	0.99[ASN][1000 genomes]
rs1662594	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662596	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1662597	0.96[ASN][1000 genomes]
rs17608961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838105	0.82[JPT][hapmap]
rs1867237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs189899	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs197912	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs197913	0.87[ASN][1000 genomes]
rs197915	0.90[ASN][1000 genomes]
rs197917	0.97[ASN][1000 genomes]
rs197918	0.99[ASN][1000 genomes]
rs197919	0.99[ASN][1000 genomes]
rs197922	0.82[JPT][hapmap]
rs197923	0.82[JPT][hapmap]
rs197925	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs197926	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003538	0.94[ASN][1000 genomes]
rs2003539	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072317	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2191033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2316330	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317997	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553405	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920396	0.99[ASN][1000 genomes]
rs2920397	0.99[ASN][1000 genomes]
rs35707546	0.96[ASN][1000 genomes]
rs3760377	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785889	0.80[GIH][hapmap]
rs3809854	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851785	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851786	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851787	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4381655	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602097	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968248	0.96[ASN][1000 genomes]
rs4968250	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968285	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968286	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968287	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968288	0.99[ASN][1000 genomes]
rs4968290	0.90[ASN][1000 genomes]
rs61671555	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs62075889	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504622	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7213526	0.97[ASN][1000 genomes]
rs7225428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7342957	0.99[ASN][1000 genomes]
rs736603	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs736604	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740617	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs758391	0.82[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs758392	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs9303532	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9889741	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889762	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893713	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9898527	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9898981	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901977	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9910899	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9911366	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9911967	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9912794	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
9	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3851784	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs3851784	GOSR2	cis	lymphoblastoid	seeQTL
rs3851784	GOSR2	cis	multi-tissue	Pritchard
rs3851784	SLC25A39	cis	cerebellum	SCAN
rs3851784	FZD2	cis	parietal	SCAN
rs3851784	MYL4	cis	multi-tissue	Pritchard
rs3851784	GOSR2	cis	normal skin	skin_eQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45021800-45051800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:45022800-45044400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr17:45022800-45045000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr17:45023000-45045400	Weak transcription	Ovary	ovary
5	chr17:45027400-45054000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:45028000-45044400	Weak transcription	Primary T cells from cord blood	blood
7	chr17:45028600-45048800	Weak transcription	Esophagus	oesophagus
8	chr17:45030400-45043800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr17:45034400-45045200	Weak transcription	HepG2	liver
10	chr17:45034600-45045600	Weak transcription	Fetal Intestine Small	intestine
11	chr17:45036400-45043600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:45036400-45045800	Weak transcription	Fetal Brain Female	brain
13	chr17:45036400-45052400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:45036600-45054400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:45037400-45055800	Weak transcription	Aorta	Aorta
16	chr17:45037800-45052200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr17:45038000-45052600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:45039400-45040200	Enhancers	NHLF	lung
19	chr17:45039600-45040200	Enhancers	NHDF-Ad	bronchial
20	chr17:45039800-45040200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:45039800-45040200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:45039800-45040200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:45039800-45040200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:45039800-45040200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr17:45039800-45040200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:45039800-45040200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr17:45039800-45040200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:45039800-45040200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr17:45039800-45040200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:45039800-45040200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:45039800-45040200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:45039800-45040200	Enhancers	Duodenum Mucosa	Duodenum
33	chr17:45039800-45040200	Enhancers	Fetal Stomach	stomach
34	chr17:45039800-45040200	Enhancers	Pancreas	Pancrea
35	chr17:45039800-45040200	Enhancers	Spleen	Spleen
36	chr17:45039800-45040200	Enhancers	GM12878-XiMat	blood
37	chr17:45039800-45040200	Bivalent Enhancer	HMEC	breast
38	chr17:45039800-45040200	Enhancers	HSMM	muscle
39	chr17:45039800-45040200	Enhancers	HSMMtube	muscle
40	chr17:45039800-45040200	Enhancers	HUVEC	blood vessel
41	chr17:45039800-45040200	Enhancers	NHEK	skin
42	chr17:45039800-45040400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:45040000-45040200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:45040000-45040200	Enhancers	Hela-S3	cervix

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