Variant report

Variant	rs859621
Chromosome Location	chr1:172687870-172687871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172686833..172688972-chr1:172691671..172694173,3	K562	blood:
2	chr1:172687416..172689203-chr1:172691086..172692709,2	MCF-7	breast:
3	chr1:172575736..172579106-chr1:172685787..172690333,5	MCF-7	breast:
4	chr1:172422603..172424142-chr1:172686598..172688545,2	K562	blood:
5	chr1:172502079..172503900-chr1:172686438..172689153,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10912460	0.89[EUR][1000 genomes]
rs1102704	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1102706	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1102707	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12136569	0.95[EUR][1000 genomes]
rs17370861	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs704845	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs859618	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859619	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859623	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859631	0.83[EUR][1000 genomes]
rs859633	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]
rs859634	0.95[EUR][1000 genomes]
rs859636	0.95[EUR][1000 genomes]
rs859637	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs859638	0.95[EUR][1000 genomes]
rs859639	0.95[EUR][1000 genomes]
rs859641	0.87[EUR][1000 genomes]
rs859643	0.95[EUR][1000 genomes]
rs859644	0.95[EUR][1000 genomes]
rs859647	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs859648	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs859673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs863578	0.85[AMR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs859621	CD247	cis	parietal	SCAN
rs859621	C1orf114	cis	cerebellum	SCAN
rs859621	ATP1B1	cis	cerebellum	SCAN
rs859621	C1orf112	cis	parietal	SCAN
rs859621	SLC9A11	cis	parietal	SCAN
rs859621	SELP	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172683400-172689200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:172684000-172688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:172684000-172688400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:172684000-172689000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:172684000-172692400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:172685000-172690400	Enhancers	Placenta	Placenta
7	chr1:172685400-172689200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:172685800-172689000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:172685800-172689000	Weak transcription	Left Ventricle	heart
10	chr1:172686000-172688400	Enhancers	Fetal Intestine Large	intestine
11	chr1:172686000-172688600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:172686000-172688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:172686000-172688600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:172686000-172693600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:172686200-172688400	Weak transcription	Dnd41	blood
16	chr1:172686200-172693800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:172686200-172693800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:172686200-172693800	Weak transcription	Fetal Thymus	thymus
19	chr1:172686400-172688400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:172686600-172688400	Enhancers	Osteobl	bone
21	chr1:172686800-172688000	Enhancers	K562	blood
22	chr1:172686800-172688600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:172686800-172688600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:172686800-172689200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:172686800-172689200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:172687000-172688400	Enhancers	HMEC	breast
27	chr1:172687000-172688800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:172687000-172689400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:172687000-172689600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:172687000-172689800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:172687200-172688200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:172687200-172689200	Enhancers	NHLF	lung
33	chr1:172687400-172689000	Weak transcription	A549	lung
34	chr1:172687600-172688600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:172687600-172689200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:172687600-172689200	Flanking Active TSS	NHEK	skin
37	chr1:172687600-172689800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:172687800-172688400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:172687800-172688600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:172687800-172688600	Enhancers	NHDF-Ad	bronchial
41	chr1:172687800-172689400	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:172687800-172692400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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