Variant report

Variant	rs3125628
Chromosome Location	chr1:47761891-47761892
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47760276..47762987-chr1:47777848..47781165,4	K562	blood:
2	chr1:47751084..47753153-chr1:47760192..47761926,2	K562	blood:
3	chr1:47755819..47758720-chr1:47758998..47762198,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10157883	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1028646	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1028647	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1044457	0.85[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs10789507	0.90[JPT][hapmap]
rs10890475	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10890476	0.82[ASN][1000 genomes]
rs10890478	0.89[JPT][hapmap]
rs11211504	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11211508	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11211510	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211511	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211513	0.90[JPT][hapmap]
rs11211517	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211520	0.89[JPT][hapmap]
rs11582877	0.90[JPT][hapmap]
rs12039726	0.90[JPT][hapmap]
rs12042624	0.82[ASN][1000 genomes]
rs12047319	0.82[ASN][1000 genomes]
rs12118514	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12121831	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12125261	0.96[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12126139	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12127982	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12132928	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12138072	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12141060	0.96[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12562561	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12730819	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12732050	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12732410	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12743877	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17452995	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2246707	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2472725	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2494247	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622901	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622905	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622907	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2622908	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622925	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742081	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742099	0.80[ASN][1000 genomes]
rs2742103	0.81[ASN][1000 genomes]
rs2742104	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2758735	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2758736	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758737	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2758744	0.81[ASN][1000 genomes]
rs2820987	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2820988	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2820989	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2821087	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2821088	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2821090	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2821093	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2821094	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2821096	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088062	0.90[JPT][hapmap]
rs3122607	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122610	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3122611	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3122615	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3122616	0.82[ASN][1000 genomes]
rs3122619	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3122620	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3122623	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3125624	0.92[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3125625	0.82[EUR][1000 genomes]
rs3125630	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3125631	0.82[ASN][1000 genomes]
rs3125632	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3125633	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3125635	0.90[JPT][hapmap]
rs3125636	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3125638	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3125639	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3125640	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3125641	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3125644	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs34400183	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34952704	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35711761	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35774681	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35880845	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3925058	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4147192	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4492666	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4926824	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4926836	0.90[JPT][hapmap]
rs55737131	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56987466	0.82[ASN][1000 genomes]
rs58688029	0.81[ASN][1000 genomes]
rs59492977	0.81[ASN][1000 genomes]
rs61782706	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61782712	0.81[ASN][1000 genomes]
rs6588348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588365	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6659946	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6660321	0.90[JPT][hapmap]
rs6671254	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6681868	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689687	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692691	0.88[GIH][hapmap]
rs6692734	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6697248	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6703956	0.96[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6795	0.85[CEU][hapmap]
rs71645861	0.85[EUR][1000 genomes]
rs7511699	0.82[ASN][1000 genomes]
rs7525650	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532148	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7541748	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543016	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9436394	0.82[ASN][1000 genomes]
rs9436429	0.82[ASN][1000 genomes]
rs9436430	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9436749	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9436838	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9436882	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3125628	CMPK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47705200-47766400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47705600-47766400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:47714400-47779200	Weak transcription	Small Intestine	intestine
4	chr1:47714600-47778400	Weak transcription	Fetal Heart	heart
5	chr1:47716600-47772600	Strong transcription	Dnd41	blood
6	chr1:47720600-47766400	Weak transcription	Brain Germinal Matrix	brain
7	chr1:47721600-47766800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:47723400-47772400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:47729000-47767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:47730400-47770200	Weak transcription	Colonic Mucosa	Colon
11	chr1:47730800-47766400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:47731400-47778000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:47735400-47779000	Weak transcription	Esophagus	oesophagus
14	chr1:47741400-47771400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:47741600-47770800	Strong transcription	Fetal Thymus	thymus
16	chr1:47741800-47770800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:47742600-47773000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:47742600-47773000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:47742800-47763800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:47743800-47766400	Weak transcription	Fetal Kidney	kidney
21	chr1:47743800-47779200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:47744200-47779000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:47744400-47779000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:47744800-47779000	Weak transcription	HSMMtube	muscle
25	chr1:47745000-47762000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:47746200-47772000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:47746200-47778800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:47746600-47765400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:47746600-47772200	Weak transcription	Ovary	ovary
30	chr1:47746600-47776400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:47746600-47778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:47746600-47778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:47746600-47778400	Weak transcription	Fetal Brain Female	brain
34	chr1:47746800-47766400	Weak transcription	NHLF	lung
35	chr1:47746800-47766600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:47746800-47768800	Weak transcription	Aorta	Aorta
37	chr1:47746800-47778800	Weak transcription	Placenta	Placenta
38	chr1:47749200-47765400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:47749400-47765200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:47749400-47765400	Weak transcription	NHDF-Ad	bronchial
41	chr1:47749400-47766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:47749600-47763200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:47749600-47766400	Weak transcription	A549	lung
44	chr1:47749600-47777800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:47750000-47779200	Weak transcription	Right Atrium	heart
46	chr1:47751000-47766600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:47751400-47765400	Weak transcription	Fetal Lung	lung
48	chr1:47751400-47766200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:47752600-47764000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:47753600-47766400	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links