Variant report

Variant	rs9817807
Chromosome Location	chr3:49442548-49442549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49441534..49443566-chr3:49445020..49447765,2	K562	blood:
2	chr3:49441705..49446563-chr3:49447849..49450189,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1009051	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10154992	1.00[ASN][1000 genomes]
rs10155014	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10452032	1.00[ASN][1000 genomes]
rs1078341	1.00[ASN][1000 genomes]
rs10865956	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106620	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11130183	1.00[ASN][1000 genomes]
rs11130186	1.00[ASN][1000 genomes]
rs11130187	1.00[ASN][1000 genomes]
rs11130190	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	1.00[ASN][1000 genomes]
rs11710434	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715060	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719762	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11720542	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923032	0.83[AMR][1000 genomes]
rs11928090	0.80[EUR][1000 genomes]
rs12583	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637313	1.00[ASN][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13096474	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1464569	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1532204	1.00[ASN][1000 genomes]
rs1586827	1.00[ASN][1000 genomes]
rs1982861	0.80[EUR][1000 genomes]
rs2029591	1.00[ASN][1000 genomes]
rs2082923	1.00[ASN][1000 genomes]
rs2099526	1.00[ASN][1000 genomes]
rs2131108	1.00[ASN][1000 genomes]
rs2140270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312462	0.80[EUR][1000 genomes]
rs2329021	1.00[ASN][1000 genomes]
rs2329025	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3020779	1.00[ASN][1000 genomes]
rs3448	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs3866330	0.80[EUR][1000 genomes]
rs3870339	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3870341	0.80[EUR][1000 genomes]
rs3905330	0.84[EUR][1000 genomes]
rs4052546	0.82[EUR][1000 genomes]
rs4241405	1.00[ASN][1000 genomes]
rs4241407	0.80[EUR][1000 genomes]
rs4384984	1.00[ASN][1000 genomes]
rs4855845	1.00[ASN][1000 genomes]
rs4855846	1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855858	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4855869	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855885	1.00[ASN][1000 genomes]
rs4955413	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4955414	1.00[ASN][1000 genomes]
rs4955421	1.00[ASN][1000 genomes]
rs4955423	1.00[ASN][1000 genomes]
rs4955424	0.89[EUR][1000 genomes]
rs4955425	0.88[EUR][1000 genomes]
rs4955427	1.00[ASN][1000 genomes]
rs4955430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	1.00[ASN][1000 genomes]
rs4955443	1.00[ASN][1000 genomes]
rs56127630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57273516	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259933	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259943	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259944	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259947	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261183	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62261249	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs6446256	1.00[ASN][1000 genomes]
rs6446257	1.00[ASN][1000 genomes]
rs6446262	0.91[EUR][1000 genomes]
rs6446275	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6769744	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6769821	1.00[ASN][1000 genomes]
rs6775069	0.90[EUR][1000 genomes]
rs6778080	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6783003	0.86[EUR][1000 genomes]
rs6784203	0.89[EUR][1000 genomes]
rs6785045	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790105	0.81[EUR][1000 genomes]
rs6796147	0.87[EUR][1000 genomes]
rs6797299	1.00[ASN][1000 genomes]
rs6805609	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808036	1.00[ASN][1000 genomes]
rs6809204	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934271	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088137	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355800	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374731	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7429661	1.00[ASN][1000 genomes]
rs7613491	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	1.00[ASN][1000 genomes]
rs7619789	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7620024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7622786	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7626076	1.00[ASN][1000 genomes]
rs7631586	1.00[ASN][1000 genomes]
rs7638750	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644148	0.83[EUR][1000 genomes]
rs7647973	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651372	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9654010	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs974495	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9757181	0.82[EUR][1000 genomes]
rs9809237	0.84[EUR][1000 genomes]
rs9812360	0.84[EUR][1000 genomes]
rs9824435	1.00[ASN][1000 genomes]
rs9830730	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	1.00[ASN][1000 genomes]
rs9842132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860055	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860285	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862534	0.80[EUR][1000 genomes]
rs9867285	1.00[ASN][1000 genomes]
rs9871024	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881860	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[ASN][1000 genomes]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9817807	AMT	cis	Nerve Tibial	GTEx
rs9817807	NICN1-AS1	cis	Thyroid	GTEx
rs9817807	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9817807	AMT	cis	Adipose Subcutaneous	GTEx
rs9817807	WDR6	cis	Muscle Skeletal	GTEx
rs9817807	AMT	cis	Esophagus Mucosa	GTEx
rs9817807	AMT	cis	Artery Tibial	GTEx
rs9817807	WDR6	cis	Nerve Tibial	GTEx
rs9817807	AMT	cis	Esophagus Muscularis	GTEx
rs9817807	NICN1	cis	Thyroid	GTEx
rs9817807	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9817807	AMT	cis	Muscle Skeletal	GTEx
rs9817807	AMT	cis	lung	GTEx
rs9817807	WDR6	cis	Esophagus Muscularis	GTEx
rs9817807	AMT	cis	Thyroid	GTEx
rs9817807	AMT	cis	Whole Blood	GTEx
rs9817807	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49413200-49443000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:49422200-49443000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:49424200-49443400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:49426000-49444000	Weak transcription	Esophagus	oesophagus
8	chr3:49426200-49443000	Weak transcription	NHLF	lung
9	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:49433800-49444000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
14	chr3:49434200-49442800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:49434800-49443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:49435400-49445600	Weak transcription	Fetal Brain Male	brain
17	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
18	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:49435600-49443000	Weak transcription	NHDF-Ad	bronchial
20	chr3:49435600-49443200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49435800-49443000	Weak transcription	Small Intestine	intestine
22	chr3:49435800-49446800	Weak transcription	Brain Angular Gyrus	brain
23	chr3:49436600-49443200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:49438200-49442800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:49438200-49443000	Weak transcription	Liver	Liver
26	chr3:49438200-49443800	Weak transcription	K562	blood
27	chr3:49438200-49444000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:49438200-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:49438800-49444000	Weak transcription	Right Ventricle	heart
30	chr3:49439000-49442800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:49439000-49443200	Weak transcription	Primary B cells from cord blood	blood
32	chr3:49439000-49447200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:49439200-49443600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:49439400-49443000	Weak transcription	Brain Substantia Nigra	brain
35	chr3:49439400-49443000	Weak transcription	Left Ventricle	heart
36	chr3:49439400-49443400	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:49439400-49444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:49439600-49443000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:49439600-49443000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:49439600-49443000	Weak transcription	HSMM	muscle
41	chr3:49439600-49443000	Weak transcription	NH-A	brain
42	chr3:49439600-49443200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:49439600-49443200	Weak transcription	Gastric	stomach
44	chr3:49439600-49443600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:49439600-49443600	Weak transcription	HepG2	liver
46	chr3:49439600-49444600	Weak transcription	Fetal Heart	heart
47	chr3:49439600-49447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:49439800-49443000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:49439800-49444200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:49439800-49447000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links