Variant report

Variant	rs9681917
Chromosome Location	chr3:47791582-47791583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1014228	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap]
rs1060407	0.89[CEU][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs10865948	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs11130138	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs11130139	0.92[CEU][hapmap]
rs11130143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs11130144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs11130148	1.00[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11707679	0.89[CEU][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap]
rs11712464	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs11716582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs12489865	1.00[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs12495204	0.84[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs12635438	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs13061412	1.00[CEU][hapmap]
rs13063042	1.00[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs13079407	1.00[CEU][hapmap]
rs13091913	1.00[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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13094264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1403578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1403579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1464614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1486915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1684942	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17079785	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs17290490	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2047559	1.00[CEU][hapmap]
rs2133601	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap]
rs2140335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2280567	1.00[CEU][hapmap]
rs2293226	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs2351248	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs2882611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs319682	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs319693	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap]
rs319694	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs319695	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs319696	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3732530	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[TSI][hapmap]
rs3755637	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs3772399	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs3888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs3915654	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4274776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs4858801	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4858842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs4858846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4858851	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4858860	1.00[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4858863	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs4858871	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs6442082	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs6763824	0.91[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs6768699	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs6772301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6774170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs6776963	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs6777632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6785669	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6786001	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs6792497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6806860	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7429162	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs7613934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7618758	0.84[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs7621236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7624474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7629850	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs7631950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7638103	1.00[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];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7645846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs777015	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs796566	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs810334	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs869508	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs870622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883662	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs883663	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9681917	SMARCC1	cis	cerebellum	SCAN
rs9681917	ZNF589	cis	cerebellum	SCAN
rs9681917	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs9681917	ATRIP	cis	cerebellum	SCAN
rs9681917	HYAL2	cis	cerebellum	SCAN
rs9681917	ZNF589	cis	parietal	SCAN
rs9681917	MAP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47701600-47800400	Strong transcription	Dnd41	blood
2	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47769600-47812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
6	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:47774200-47792600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47774200-47799000	Weak transcription	NHEK	skin
9	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:47777200-47794000	Weak transcription	Psoas Muscle	Psoas
12	chr3:47777200-47801400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:47777200-47805200	Weak transcription	Esophagus	oesophagus
14	chr3:47777200-47812400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:47777200-47813600	Weak transcription	A549	lung
16	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
17	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
18	chr3:47777400-47799600	Weak transcription	Spleen	Spleen
19	chr3:47777400-47802000	Weak transcription	Aorta	Aorta
20	chr3:47777400-47805400	Weak transcription	Gastric	stomach
21	chr3:47777400-47805600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:47777400-47812600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:47777400-47819800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:47777400-47821000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:47777400-47821000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:47777400-47821800	Weak transcription	Right Ventricle	heart
27	chr3:47777600-47798200	Weak transcription	Brain Anterior Caudate	brain
28	chr3:47777600-47812800	Weak transcription	NHDF-Ad	bronchial
29	chr3:47777600-47820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:47777600-47820800	Weak transcription	NHLF	lung
31	chr3:47777800-47802000	Weak transcription	Fetal Kidney	kidney
32	chr3:47778800-47798200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:47778800-47805400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:47778800-47814200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:47781200-47802600	Weak transcription	Ovary	ovary
36	chr3:47784000-47816000	Strong transcription	Fetal Stomach	stomach
37	chr3:47784400-47811800	Weak transcription	Left Ventricle	heart
38	chr3:47784600-47793800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:47784800-47799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:47784800-47820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:47785200-47805400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:47785600-47798200	Weak transcription	Hela-S3	cervix
43	chr3:47785600-47803600	Weak transcription	Fetal Heart	heart
44	chr3:47786200-47793600	Strong transcription	Fetal Intestine Small	intestine
45	chr3:47786400-47805400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:47786600-47794200	Weak transcription	Liver	Liver
47	chr3:47786600-47805000	Weak transcription	HMEC	breast
48	chr3:47786600-47814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:47786800-47793800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:47786800-47793800	Weak transcription	NH-A	brain

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