Variant report

Variant	rs859648
Chromosome Location	chr1:172696653-172696654
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	chr1:172578385..172579260-chr1:172696065..172697862,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10912460	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1102704	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102706	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102707	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581258	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs11587368	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs12136569	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704845	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859618	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs859619	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs859621	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs859622	0.85[TSI][hapmap]
rs859623	0.87[EUR][1000 genomes]
rs859629	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs859631	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859633	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859634	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859636	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859637	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859638	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859639	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859641	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859643	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859644	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859647	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859673	0.86[EUR][1000 genomes]
rs863578	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs974856	0.82[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs859648	SLC9A11	cis	parietal	SCAN
rs859648	C1orf112	cis	parietal	SCAN
rs859648	SELP	cis	cerebellum	SCAN
rs859648	C1orf114	cis	cerebellum	SCAN
rs859648	CD247	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172689200-172696800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:172689200-172700400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:172693400-172712200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172693800-172697400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:172694600-172697400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:172695800-172697000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:172696000-172696800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:172696000-172697200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:172696000-172697600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:172696400-172696800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:172696400-172696800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:172696600-172696800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links