Variant report

Variant	rs1345156
Chromosome Location	chr3:160649272-160649273
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160473266..160475652-chr3:160647072..160650166,3	MCF-7	breast:
2	chr3:160643537..160645831-chr3:160647633..160653129,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs11711152	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs11713093	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11717272	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs11718966	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11720263	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs11916355	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690576	0.87[JPT][hapmap]
rs13060718	0.81[EUR][1000 genomes]
rs13071999	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13256	0.90[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs13315565	0.94[CEU][hapmap]
rs1447610	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1447622	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1562464	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16831563	0.84[EUR][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs1839016	0.86[EUR][1000 genomes]
rs1868105	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs2044571	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4521287	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs4679920	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6441337	0.84[EUR][1000 genomes]
rs6441338	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs66872845	0.90[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs6774725	1.00[CEU][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6801444	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs733948	0.83[CHD][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap]
rs7624185	1.00[CEU][hapmap];0.97[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7628389	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7641892	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs898677	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs935497	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9822435	1.00[CEU][hapmap]
rs9832109	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs9844267	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs9845943	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9857482	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9857855	0.84[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871801	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs9883566	0.90[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1345156	C3orf57	cis	parietal	SCAN
rs1345156	PPM1L	cis	cerebellum	SCAN
rs1345156	B3GALNT1	cis	lymphoblastoid	seeQTL
rs1345156	NMD3	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160644800-160654400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:160647200-160650200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:160647600-160650400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:160647600-160652400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:160648000-160653200	Weak transcription	Adipose Nuclei	Adipose
6	chr3:160648400-160650200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:160648400-160650400	Enhancers	NHDF-Ad	bronchial
8	chr3:160648600-160649400	Enhancers	Fetal Heart	heart
9	chr3:160648800-160650600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:160649000-160649600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:160649000-160650200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160649000-160650200	Enhancers	NHLF	lung
13	chr3:160649200-160649400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:160649200-160649400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:160649200-160649400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:160649200-160649400	Enhancers	Stomach Smooth Muscle	stomach
17	chr3:160649200-160650600	Enhancers	Fetal Brain Female	brain
18	chr3:160649200-160651400	Weak transcription	Fetal Brain Male	brain

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