Variant report

Variant	rs1523130
Chromosome Location	chr3:119499507-119499508
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	chr3:119498195..119499801-chr3:119500089..119502246,2	K562	blood:
2	chr3:119498195..119499776-chr3:119500089..119502545,2	K562	blood:

Variant related genes	Relation type
ENSG00000144852	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10511394	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs10934498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129708	0.82[ASN][1000 genomes]
rs11926554	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12488820	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13089523	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464599	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1523127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1581451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608330	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608332	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2461829	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2461830	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472664	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472674	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34255376	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34787921	0.83[ASN][1000 genomes]
rs35576922	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4566573	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66840889	0.81[ASN][1000 genomes]
rs7642839	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289134	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs9817024	0.83[ASN][1000 genomes]
rs9821892	0.83[ASN][1000 genomes]
rs9832958	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865270	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1523130	COX17	cis	lymphoblastoid	seeQTL
rs1523130	C3orf15	cis	lymphoblastoid	seeQTL
rs1523130	HSPBAP1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119497800-119503000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr3:119498000-119499600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:119498000-119499600	Enhancers	GM12878-XiMat	blood
4	chr3:119498200-119501000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:119498400-119499600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:119498600-119499600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr3:119498600-119499800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:119498800-119499600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:119498800-119500000	Enhancers	HepG2	liver
10	chr3:119498800-119500400	Enhancers	Liver	Liver
11	chr3:119498800-119500600	Enhancers	Fetal Intestine Large	intestine
12	chr3:119498800-119500600	Enhancers	Fetal Intestine Small	intestine
13	chr3:119499000-119500400	Weak transcription	Spleen	Spleen
14	chr3:119499200-119500000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr3:119499200-119501800	Weak transcription	K562	blood
16	chr3:119499200-119502000	Weak transcription	HSMMtube	muscle
17	chr3:119499400-119501200	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links