Variant report

Variant	rs579989
Chromosome Location	chr1:172138326-172138327
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172137145..172139186-chr1:173835377..173837374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10489298	0.92[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs12125882	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843944	0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs16843959	0.91[ASN][1000 genomes]
rs16843972	0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1746427	0.92[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs1746428	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209097	0.93[ASN][1000 genomes]
rs2761189	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2819529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480988	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs490006	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs491767	0.93[ASN][1000 genomes]
rs499106	0.92[ASN][1000 genomes]
rs510473	0.93[ASN][1000 genomes]
rs511520	0.90[ASN][1000 genomes]
rs514864	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs515060	0.92[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs532688	0.95[JPT][hapmap]
rs535441	0.92[ASN][1000 genomes]
rs537444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546751	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs552191	0.92[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs552399	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567168	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570742	0.93[ASN][1000 genomes]
rs572802	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586745	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs589245	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590567	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598562	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs598577	0.85[ASN][1000 genomes]
rs608156	0.92[ASN][1000 genomes]
rs610082	0.93[ASN][1000 genomes]
rs610587	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs615091	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61633880	0.93[ASN][1000 genomes]
rs624538	0.93[ASN][1000 genomes]
rs629316	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629762	0.93[ASN][1000 genomes]
rs631915	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633995	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs640159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651032	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs672740	0.80[CEU][hapmap]
rs676081	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676215	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676597	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682215	0.93[ASN][1000 genomes]
rs683128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688451	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912299	0.84[CEU][hapmap]
rs9425500	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425501	0.87[AMR][1000 genomes]
rs9425503	0.93[ASN][1000 genomes]
rs9425504	0.93[ASN][1000 genomes]
rs9425505	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172123400-172149200	Weak transcription	Brain Anterior Caudate	brain
2	chr1:172128400-172149800	Weak transcription	Aorta	Aorta
3	chr1:172132800-172150000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:172134000-172139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:172134800-172139400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:172136800-172138600	Enhancers	Brain Hippocampus Middle	brain
7	chr1:172136800-172140400	Enhancers	Fetal Heart	heart
8	chr1:172137000-172138600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:172137000-172138600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:172137000-172138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:172137000-172138800	Enhancers	NHDF-Ad	bronchial
12	chr1:172137000-172139200	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:172137000-172139600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:172137000-172139800	Enhancers	Fetal Lung	lung
15	chr1:172137200-172138400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:172137200-172138400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:172137200-172138600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:172137200-172138600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:172137200-172138600	Enhancers	HMEC	breast
20	chr1:172137400-172138600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:172137400-172138600	Enhancers	Fetal Intestine Large	intestine
22	chr1:172137400-172138800	Enhancers	Brain Substantia Nigra	brain
23	chr1:172137400-172140200	Enhancers	Fetal Intestine Small	intestine
24	chr1:172137600-172138400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:172137600-172138400	Enhancers	Osteobl	bone
26	chr1:172137600-172138600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:172137600-172138600	Enhancers	Small Intestine	intestine
28	chr1:172137800-172138600	Enhancers	Fetal Stomach	stomach
29	chr1:172138000-172138600	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:172138000-172141200	Weak transcription	Right Ventricle	heart
31	chr1:172138000-172141400	Weak transcription	HSMM	muscle
32	chr1:172138000-172141400	Weak transcription	NHLF	lung
33	chr1:172138000-172143600	Weak transcription	Fetal Brain Male	brain
34	chr1:172138200-172147800	Weak transcription	Brain Angular Gyrus	brain

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