Variant report

Variant	rs811794
Chromosome Location	chr3:138170961-138170962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138152067..138153775-chr3:138169983..138172416,2	MCF-7	breast:
2	chr3:138169355..138171117-chr3:138172389..138174530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11916525	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12054428	0.84[EUR][1000 genomes]
rs12630060	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12631438	0.91[JPT][hapmap]
rs12632793	1.00[CEU][hapmap]
rs12632794	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12633098	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12635490	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12635904	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12637679	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12638938	0.92[EUR][1000 genomes]
rs13059817	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs13062423	0.91[JPT][hapmap]
rs13084780	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs13098554	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs1546758	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs1563615	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs1679153	0.86[JPT][hapmap]
rs1679181	0.91[JPT][hapmap]
rs1720829	0.91[JPT][hapmap]
rs4678418	0.95[ASN][1000 genomes]
rs6768963	1.00[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7611650	0.96[EUR][1000 genomes]
rs774014	0.96[EUR][1000 genomes]
rs812277	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs9049	1.00[CEU][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:138162400-138177200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:138162800-138178800	Weak transcription	Fetal Intestine Small	intestine
6	chr3:138163600-138173800	Weak transcription	Lung	lung
7	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:138167800-138171200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:138168600-138171800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:138169200-138172400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:138169400-138171600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:138169400-138173800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:138169600-138172400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:138169600-138172400	Enhancers	Placenta	Placenta
15	chr3:138169800-138171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:138169800-138171200	Enhancers	Spleen	Spleen
17	chr3:138169800-138171400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:138169800-138171800	Enhancers	HMEC	breast
19	chr3:138169800-138174000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:138170000-138171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:138170000-138171200	Weak transcription	NHEK	skin
22	chr3:138170000-138171400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:138170200-138171400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:138170200-138174200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:138170400-138171000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:138170600-138171600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr3:138170800-138171600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links