Variant report

Variant	rs3772879
Chromosome Location	chr3:139179909-139179910
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139164444..139166894-chr3:139178847..139180451,2	K562	blood:
2	chr3:139178292..139180286-chr3:139183692..139185516,2	K562	blood:

Variant related genes	Relation type
ENSG00000248790	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1044826	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10460845	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10935320	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10935323	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12488939	0.83[ASN][1000 genomes]
rs12494556	0.87[ASN][1000 genomes]
rs12494806	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12695698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12695699	0.97[ASN][1000 genomes]
rs12695700	0.88[ASN][1000 genomes]
rs13060697	0.90[ASN][1000 genomes]
rs13074208	0.88[ASN][1000 genomes]
rs13083195	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13085888	0.95[ASN][1000 genomes]
rs13086868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13089007	0.95[ASN][1000 genomes]
rs13089052	0.87[ASN][1000 genomes]
rs13089090	0.93[ASN][1000 genomes]
rs13092507	0.85[ASN][1000 genomes]
rs13092935	0.97[ASN][1000 genomes]
rs1586861	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1586863	0.88[ASN][1000 genomes]
rs1586864	0.88[ASN][1000 genomes]
rs17336869	0.98[ASN][1000 genomes]
rs1907687	0.88[ASN][1000 genomes]
rs2165139	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2233811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2233815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2349059	0.95[ASN][1000 genomes]
rs34623690	0.98[ASN][1000 genomes]
rs3772877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3772878	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3821544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3821545	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4544576	0.88[ASN][1000 genomes]
rs4683818	0.87[ASN][1000 genomes]
rs67929453	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs747346	0.87[ASN][1000 genomes]
rs9289576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs964227	0.88[ASN][1000 genomes]
rs973691	0.98[ASN][1000 genomes]
rs9812192	0.95[ASN][1000 genomes]
rs9818691	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9825064	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9831108	0.83[CHB][hapmap];0.95[ASN][1000 genomes]
rs9834607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9835241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9848241	0.88[ASN][1000 genomes]
rs9849039	0.88[ASN][1000 genomes]
rs9849578	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9853350	0.95[ASN][1000 genomes]
rs9860201	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9860521	0.88[ASN][1000 genomes]
rs9868544	0.95[ASN][1000 genomes]
rs9882014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1000519	chr3:139159300-139206245	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2752377	chr3:139163302-139188302	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139163400-139189000	Weak transcription	Small Intestine	intestine
2	chr3:139163800-139180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:139168600-139196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:139171200-139210200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:139173800-139180600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:139173800-139180600	Weak transcription	Pancreas	Pancrea
7	chr3:139175600-139180600	Strong transcription	Fetal Intestine Small	intestine
8	chr3:139176000-139181800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:139176200-139180600	Weak transcription	Esophagus	oesophagus
10	chr3:139178200-139180600	Weak transcription	Stomach Mucosa	stomach
11	chr3:139178400-139180400	Enhancers	Fetal Muscle Leg	muscle
12	chr3:139179000-139180000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:139179200-139180600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:139179200-139180800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:139179400-139180000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:139179400-139181600	Genic enhancers	Duodenum Mucosa	Duodenum
17	chr3:139179600-139180800	Weak transcription	HMEC	breast
18	chr3:139179800-139181800	Genic enhancers	Fetal Intestine Large	intestine
19	chr3:139179800-139182200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:139179800-139196600	Weak transcription	Ovary	ovary

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