Variant report

Variant	rs6662189
Chromosome Location	chr1:47854215-47854216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47853693..47855122-chr1:47889679..47890765,13	MCF-7	breast:
2	chr1:47854116..47855124-chr1:48191664..48192613,6	K562	blood:
3	chr1:47850084..47851771-chr1:47852483..47854951,2	K562	blood:
4	chr1:47835984..47838590-chr1:47852987..47854829,2	K562	blood:
5	chr1:47854167..47855150-chr1:48175198..48176770,5	K562	blood:
6	chr1:47854121..47854805-chr1:47890169..47890734,3	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10157883	0.95[JPT][hapmap]
rs10437097	0.81[EUR][1000 genomes]
rs10789507	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10890475	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10890476	0.82[AMR][1000 genomes]
rs10890477	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10890478	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11211504	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11211508	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs11211513	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11211517	0.90[JPT][hapmap]
rs11211520	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11211521	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11211522	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11211523	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11211524	0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11578038	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11582877	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12024163	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12039726	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12040451	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12042624	0.82[AMR][1000 genomes]
rs12047319	0.82[AMR][1000 genomes]
rs12048407	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12407746	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12566521	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2306470	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406102	0.88[EUR][1000 genomes]
rs2406105	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472725	0.91[JPT][hapmap]
rs2494246	0.84[ASN][1000 genomes]
rs2622925	0.91[JPT][hapmap]
rs2742104	0.95[JPT][hapmap]
rs2758735	0.95[JPT][hapmap]
rs2820971	0.81[JPT][hapmap]
rs2820983	0.88[EUR][1000 genomes]
rs2820989	0.91[JPT][hapmap]
rs2821088	0.95[JPT][hapmap]
rs2821093	0.91[JPT][hapmap]
rs3088062	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3122607	0.95[JPT][hapmap]
rs3122611	0.95[JPT][hapmap]
rs3122615	0.95[JPT][hapmap]
rs3122619	0.95[JPT][hapmap]
rs3125624	0.95[JPT][hapmap]
rs3125628	0.84[JPT][hapmap]
rs3125630	0.95[JPT][hapmap]
rs3125632	0.91[JPT][hapmap]
rs3125633	0.90[JPT][hapmap]
rs3125635	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3125636	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs3125644	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3814003	0.83[EUR][1000 genomes]
rs3925058	0.95[JPT][hapmap]
rs4492666	0.95[JPT][hapmap]
rs4600090	0.91[YRI][hapmap]
rs4926836	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4926839	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56987466	0.82[AMR][1000 genomes]
rs61284456	0.81[ASN][1000 genomes]
rs61784774	0.84[AMR][1000 genomes]
rs6588348	0.91[JPT][hapmap]
rs6660321	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662814	0.87[ASN][1000 genomes]
rs6671254	0.95[JPT][hapmap]
rs6679121	0.87[EUR][1000 genomes]
rs6690084	0.91[YRI][hapmap]
rs6697248	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6699343	0.85[EUR][1000 genomes]
rs7525650	0.91[JPT][hapmap]
rs7532148	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7534571	0.91[YRI][hapmap]
rs7541522	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9436430	0.91[JPT][hapmap]
rs9436882	0.95[JPT][hapmap]

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47800600-47854600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47827800-47854800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:47836400-47854400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:47836600-47854800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:47841600-47854800	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:47845400-47854400	Weak transcription	HMEC	breast
7	chr1:47845600-47854400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:47847000-47854400	Weak transcription	Colonic Mucosa	Colon
9	chr1:47847000-47854600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:47847000-47854600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:47847400-47858600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:47847600-47854800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:47847600-47858800	Weak transcription	HSMMtube	muscle
14	chr1:47847600-47865200	Weak transcription	GM12878-XiMat	blood
15	chr1:47847600-47872800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:47848400-47854400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:47849000-47854400	Weak transcription	Liver	Liver
18	chr1:47849200-47855800	Weak transcription	Dnd41	blood
19	chr1:47849400-47856200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:47849400-47858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:47849600-47856000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:47852600-47855000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:47853000-47854400	Enhancers	Fetal Muscle Leg	muscle
24	chr1:47853000-47856000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:47853200-47854600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:47853200-47855000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:47853200-47857400	Enhancers	HepG2	liver
28	chr1:47853400-47854800	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:47853400-47854800	Enhancers	NHLF	lung
30	chr1:47853400-47855000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:47853400-47855200	Enhancers	Fetal Stomach	stomach
32	chr1:47853400-47856600	Enhancers	Fetal Intestine Large	intestine
33	chr1:47853400-47856600	Enhancers	Fetal Intestine Small	intestine
34	chr1:47853600-47855000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:47853600-47855600	Enhancers	Adipose Nuclei	Adipose
36	chr1:47854000-47855200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr1:47854200-47854400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:47854200-47854400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:47854200-47854400	Enhancers	Esophagus	oesophagus
40	chr1:47854200-47854400	Enhancers	Fetal Brain Female	brain
41	chr1:47854200-47854400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
42	chr1:47854200-47854400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
43	chr1:47854200-47854400	Enhancers	Right Ventricle	heart
44	chr1:47854200-47854400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
45	chr1:47854200-47854400	Enhancers	HSMM	muscle
46	chr1:47854200-47854600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
47	chr1:47854200-47854600	Bivalent Enhancer	Fetal Heart	heart
48	chr1:47854200-47854600	Enhancers	Gastric	stomach
49	chr1:47854200-47854600	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:47854200-47854600	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links