Variant report

Variant	rs859633
Chromosome Location	chr1:172712424-172712425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172711457..172712657-chr1:173377723..173378540,3	MCF-7	breast:
2	chr1:172711900..172714556-chr1:173831584..173833588,3	MCF-7	breast:
3	chr1:172410499..172413475-chr1:172711995..172715469,3	K562	blood:
4	chr1:172712052..172713758-chr1:173835242..173837024,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000270084	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10912460	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1102704	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1102706	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1102707	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581258	0.82[JPT][hapmap]
rs11587368	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs12136569	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704845	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859618	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs859619	0.85[EUR][1000 genomes]
rs859621	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs859622	0.80[TSI][hapmap]
rs859623	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs859629	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs859631	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs859634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859637	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859638	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859639	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859641	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859644	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859647	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859648	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859673	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs863578	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs974856	0.82[JPT][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs859633	ATP1B1	cis	cerebellum	SCAN
rs859633	C1orf114	cis	cerebellum	SCAN
rs859633	SELP	cis	cerebellum	SCAN
rs859633	SLC9A11	cis	parietal	SCAN
rs859633	C1orf112	cis	parietal	SCAN
rs859633	CD247	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172711400-172714000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:172712000-172712600	Enhancers	Hela-S3	cervix
3	chr1:172712000-172712800	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:172712000-172712800	Enhancers	NHLF	lung
5	chr1:172712000-172714000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:172712000-172714000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:172712000-172716400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:172712000-172716400	Enhancers	HMEC	breast
9	chr1:172712000-172717000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:172712200-172712600	Enhancers	HUVEC	blood vessel
11	chr1:172712200-172712800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:172712200-172712800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:172712200-172716400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:172712400-172712600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:172712400-172714000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:172712400-172714400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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