Variant report

Variant	rs17560106
Chromosome Location	chr3:139180230-139180231
allele	A/G
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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10513063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1602626	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1602628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17316181	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17335312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17394620	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17395611	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17494356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17494482	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs184156	1.00[JPT][hapmap]
rs1844977	0.85[ASN][1000 genomes]
rs2289348	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289350	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2307031	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2882080	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2882081	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs295490	0.89[CEU][hapmap]
rs3772871	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3772876	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397940	0.89[CEU][hapmap]
rs41356949	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41399544	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55922868	0.80[ASN][1000 genomes]
rs56993164	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57707457	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57995350	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58060926	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59628512	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59958973	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59960641	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61034702	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61613889	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61680644	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7428398	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9821204	1.00[JPT][hapmap]
rs9862672	1.00[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	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:18 , 50 per page) page: 1

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

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