Variant report

Variant	rs3819114
Chromosome Location	chr11:73971403-73971404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73970088..73972643-chr11:73975001..73976795,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10219237	0.88[MEX][hapmap]
rs10431176	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap]
rs10501415	0.84[CHB][hapmap]
rs10898955	0.84[CHB][hapmap]
rs10898957	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs10898960	0.84[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898961	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898962	0.92[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap]
rs10898963	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898964	0.81[EUR][1000 genomes]
rs10898966	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898973	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10898974	0.84[CHB][hapmap]
rs10898975	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs10898976	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11235994	0.84[CHB][hapmap];0.95[CHD][hapmap]
rs11235995	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs11235996	0.84[CHB][hapmap]
rs11236000	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs11236003	0.84[CHB][hapmap]
rs11236026	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236027	0.83[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236029	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap]
rs11236042	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs11236043	0.84[CHB][hapmap]
rs11236053	0.85[CHD][hapmap]
rs11236055	0.85[EUR][1000 genomes]
rs11600314	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602451	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11604125	0.84[CHB][hapmap]
rs11604713	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606804	0.84[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11608147	0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[TSI][hapmap]
rs12222213	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12223320	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs12225446	0.80[CHB][hapmap]
rs12574038	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs12574039	0.84[CHB][hapmap]
rs12574047	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs12574556	0.84[CHB][hapmap]
rs12574650	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12575211	0.84[CHB][hapmap]
rs1405653	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1405654	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17132715	0.84[CHB][hapmap]
rs1944971	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2091436	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2178000	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282488	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs2302508	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741132	0.84[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3741133	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3814724	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3888908	0.85[EUR][1000 genomes]
rs3894652	0.85[EUR][1000 genomes]
rs4019299	0.84[CHB][hapmap]
rs4121668	0.84[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4539349	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4565925	0.84[CHB][hapmap];0.92[CHD][hapmap]
rs58852370	0.85[EUR][1000 genomes]
rs61902362	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7110734	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[TSI][hapmap]
rs7115407	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7117465	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7125032	0.84[CHB][hapmap];0.97[CHD][hapmap]
rs7949639	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7951290	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951617	0.83[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3819114	FAM168A	cis	parietal	SCAN
rs3819114	DNAJB13	cis	cerebellum	SCAN
rs3819114	PGM2L1	cis	multi-tissue	Pritchard
rs3819114	UCP2	cis	multi-tissue	Pritchard
rs3819114	STARD10	cis	parietal	SCAN
rs3819114	PPME1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73966000-73971800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:73966000-73972000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:73966200-73980000	Weak transcription	Gastric	stomach
4	chr11:73966400-73979200	Weak transcription	Primary T cells from cord blood	blood
5	chr11:73966600-73972000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr11:73967000-73971800	Weak transcription	Liver	Liver
7	chr11:73968000-73979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:73968200-73973600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:73969400-73987600	Weak transcription	NH-A	brain
10	chr11:73969600-73972400	Enhancers	Placenta	Placenta
11	chr11:73969600-73974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:73969800-73978200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:73969800-73980400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:73970000-73980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:73970000-73987600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:73970200-73972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:73970600-73978000	Weak transcription	Hela-S3	cervix
18	chr11:73971200-73971600	Enhancers	Fetal Muscle Leg	muscle
19	chr11:73971400-73975400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:73971400-73975600	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links