Variant report

Variant	rs6663690
Chromosome Location	chr1:85705801-85705802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85574806..85575788-chr1:85705239..85706783,9	MCF-7	breast:
2	chr1:85410308..85411228-chr1:85705720..85706844,7	MCF-7	breast:
3	chr1:85574818..85575693-chr1:85705751..85706603,4	MCF-7	breast:
4	chr1:85574980..85575495-chr1:85705766..85706699,2	K562	blood:
5	chr1:85666584..85668196-chr1:85704539..85707139,2	MCF-7	breast:
6	chr1:85409879..85410688-chr1:85705752..85706654,2	K562	blood:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493762	0.83[JPT][hapmap]
rs11161556	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161574	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161584	0.88[EUR][1000 genomes]
rs11577656	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563295	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17122364	0.84[JPT][hapmap]
rs17123650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054238	0.83[JPT][hapmap]
rs2252408	0.93[EUR][1000 genomes]
rs2647396	0.89[JPT][hapmap]
rs2735587	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735591	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735592	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2735593	0.83[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs2735594	0.83[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs36006436	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907139	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4949892	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949926	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60156243	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693365	0.90[EUR][1000 genomes]
rs709790	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs72722616	0.83[ASN][1000 genomes]
rs72722624	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72722631	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72722638	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72722641	0.97[ASN][1000 genomes]
rs72722643	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7531640	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6663690	BCL10	cis	multi-tissue	Pritchard
rs6663690	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85687000-85709600	Weak transcription	Aorta	Aorta
2	chr1:85705200-85707800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:85705400-85707200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85705600-85706000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr1:85705600-85706200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:85705600-85706600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:85705600-85706600	Enhancers	Fetal Heart	heart
8	chr1:85705600-85706600	Enhancers	HSMM	muscle
9	chr1:85705600-85706800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:85705600-85707000	Enhancers	Colon Smooth Muscle	Colon
11	chr1:85705600-85707000	Enhancers	Osteobl	bone
12	chr1:85705600-85707200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:85705600-85707200	Enhancers	Fetal Lung	lung
14	chr1:85705600-85707800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:85705800-85706000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:85705800-85706000	Enhancers	Pancreas	Pancrea
17	chr1:85705800-85706400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:85705800-85706400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:85705800-85706600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:85705800-85707000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:85705800-85707000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:85705800-85707000	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:85705800-85707000	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:85705800-85707200	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links