Variant report

Variant	rs1523127
Chromosome Location	chr3:119501039-119501040
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr3:119500620-119501170	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:119500832-119501067	HepG2	liver:	n/a	n/a
3	HEY1	chr3:119500766-119501097	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:119500841-119501045	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:119500772-119501041	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:119500639-119501542	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119498195..119499776-chr3:119500089..119502545,2	K562	blood:
2	chr3:119498195..119499801-chr3:119500089..119502246,2	K562	blood:

Variant related genes	Relation type
NR1I2	TF binding region
ENSG00000144852	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511394	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs10934498	0.89[ASW][hapmap];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];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129708	0.81[ASN][1000 genomes]
rs11926554	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12488820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089523	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1464599	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1523130	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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1608330	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1608332	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2461829	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2461830	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472664	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472674	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34255376	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787921	0.82[ASN][1000 genomes]
rs35576922	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4566573	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7642839	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289134	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs9817024	0.82[ASN][1000 genomes]
rs9821892	0.82[ASN][1000 genomes]
rs9832958	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865270	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1523127	HSPBAP1	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr3:119499200-119501800	Weak transcription	K562	blood
3	chr3:119499200-119502000	Weak transcription	HSMMtube	muscle
4	chr3:119499400-119501200	Weak transcription	HSMM	muscle
5	chr3:119499600-119501600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:119499600-119501800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:119499600-119502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:119500000-119503200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:119500200-119514400	Weak transcription	Small Intestine	intestine
10	chr3:119500400-119502400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:119500600-119502400	Active TSS	Colonic Mucosa	Colon
12	chr3:119500600-119502800	Active TSS	Fetal Intestine Small	intestine
13	chr3:119500600-119503400	Active TSS	Liver	Liver
14	chr3:119500600-119504000	Active TSS	Fetal Intestine Large	intestine
15	chr3:119500600-119504400	Active TSS	Duodenum Mucosa	Duodenum
16	chr3:119500800-119501400	Bivalent/Poised TSS	HepG2	liver
17	chr3:119501000-119501200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr3:119501000-119501400	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr3:119501000-119501800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:119501000-119501800	Flanking Active TSS	Stomach Mucosa	stomach
21	chr3:119501000-119502000	Active TSS	Rectal Smooth Muscle	rectum
22	chr3:119501000-119502400	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links