Variant report

Variant	rs16969038
Chromosome Location	chr15:39748389-39748390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39739352..39742846-chr15:39745277..39748876,4	MCF-7	breast:
2	chr15:39743414..39749749-chr15:39871400..39878085,10	MCF-7	breast:
3	chr15:39746552..39749195-chr15:39826550..39828305,2	MCF-7	breast:
4	chr15:39745636..39749475-chr15:39752031..39754404,4	K562	blood:
5	chr15:39742666..39745111-chr15:39746881..39749174,2	K562	blood:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10459586	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10520130	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070198	0.83[ASN][1000 genomes]
rs11070206	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070207	0.91[ASN][1000 genomes]
rs1158915	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158916	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1158917	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854059	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855543	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855977	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11855990	0.91[ASN][1000 genomes]
rs11857970	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1551945	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16952151	1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs16969104	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3889532	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4286083	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4923830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924362	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5028679	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56839831	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56869025	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57248361	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58417285	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61648928	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7171244	0.82[MEX][hapmap]
rs7171584	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178351	0.82[MEX][hapmap]
rs73393497	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7350779	0.82[MEX][hapmap]
rs8025111	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032303	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8034569	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv511556	chr15:39744272-39748389	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:39744400-39748400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:39744600-39753400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:39745400-39748800	Enhancers	Osteobl	bone
5	chr15:39745400-39749600	Enhancers	Fetal Lung	lung
6	chr15:39745600-39748400	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:39745600-39748400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr15:39745600-39748600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:39745600-39748800	Enhancers	NHDF-Ad	bronchial
10	chr15:39745600-39749000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:39745800-39749400	Enhancers	Adipose Nuclei	Adipose
12	chr15:39745800-39749600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:39746000-39748600	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:39746400-39748400	Enhancers	K562	blood
15	chr15:39746600-39748600	Weak transcription	Fetal Stomach	stomach
16	chr15:39746800-39748800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:39747000-39748400	Enhancers	A549	lung
18	chr15:39747400-39748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:39747600-39748600	Enhancers	NHLF	lung
20	chr15:39747600-39748800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr15:39747600-39748800	Enhancers	Stomach Mucosa	stomach
22	chr15:39748000-39749000	Enhancers	HepG2	liver
23	chr15:39748200-39753400	Weak transcription	HSMMtube	muscle
24	chr15:39748200-39753800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:39748200-39754000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links