Variant report

Variant	rs41356949
Chromosome Location	chr3:139188422-139188423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139187703..139190427-chr3:139192772..139195214,2	K562	blood:
2	chr3:139186237..139189203-chr3:139191374..139194272,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10513063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1602626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1602628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17316181	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17335312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17394620	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17395611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17494356	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17494482	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17560106	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184156	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs184157	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs1844977	0.85[ASN][1000 genomes]
rs2289348	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2307031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][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	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs3772871	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3772876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397940	0.81[CEU][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs41399544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55922868	0.80[ASN][1000 genomes]
rs56993164	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57707457	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57995350	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58060926	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59628512	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59958973	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs59960641	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61034702	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61613889	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61680644	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782727	0.82[ASW][hapmap]
rs7428398	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9821204	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9862672	1.00[CHB][hapmap];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	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 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	chr3:139179800-139196600	Weak transcription	Ovary	ovary
5	chr3:139183400-139189400	Enhancers	Fetal Lung	lung
6	chr3:139188000-139188600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr3:139188000-139189800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
8	chr3:139188400-139189000	Active TSS	Fetal Intestine Large	intestine

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