Variant report

Variant	rs12593294
Chromosome Location	chr15:39747754-39747755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39744731..39747916-chr15:39873044..39877161,3	MCF-7	breast:
2	chr15:39739352..39742846-chr15:39745277..39748876,4	MCF-7	breast:
3	chr15:39743414..39749749-chr15:39871400..39878085,10	MCF-7	breast:
4	chr15:39746552..39749195-chr15:39826550..39828305,2	MCF-7	breast:
5	chr15:39745636..39749475-chr15:39752031..39754404,4	K562	blood:
6	chr15:39742666..39745111-chr15:39746881..39749174,2	K562	blood:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11070204	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158918	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631986	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs11633970	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857561	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899217	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1812583	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1947782	0.80[ASN][1000 genomes]
rs1993892	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1993893	0.91[ASN][1000 genomes]
rs2086166	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2127029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411293	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34329697	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4486853	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4533261	0.83[YRI][hapmap]
rs4924361	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924363	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59431794	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60697424	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171244	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7180041	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7350779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74008200	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74010438	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030260	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8032900	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs8033214	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040790	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs9888722	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920130	0.85[AFR][1000 genomes]
rs9920539	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv569224	chr15:39744272-39748158	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv511556	chr15:39744272-39748389	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv569226	chr15:39744425-39748158	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 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	chr15:39745400-39747800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:39745400-39748800	Enhancers	Osteobl	bone
6	chr15:39745400-39749600	Enhancers	Fetal Lung	lung
7	chr15:39745600-39748200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:39745600-39748400	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:39745600-39748400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr15:39745600-39748600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:39745600-39748800	Enhancers	NHDF-Ad	bronchial
12	chr15:39745600-39749000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:39745800-39749400	Enhancers	Adipose Nuclei	Adipose
14	chr15:39745800-39749600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:39746000-39748000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:39746000-39748600	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:39746400-39748400	Enhancers	K562	blood
18	chr15:39746600-39748600	Weak transcription	Fetal Stomach	stomach
19	chr15:39746800-39748200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:39746800-39748200	Enhancers	HSMMtube	muscle
21	chr15:39746800-39748800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:39747000-39747800	Enhancers	GM12878-XiMat	blood
23	chr15:39747000-39748400	Enhancers	A549	lung
24	chr15:39747200-39747800	Enhancers	HMEC	breast
25	chr15:39747400-39748200	Enhancers	NH-A	brain
26	chr15:39747400-39748400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:39747600-39748000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:39747600-39748000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr15:39747600-39748000	Flanking Active TSS	HepG2	liver
30	chr15:39747600-39748600	Enhancers	NHLF	lung
31	chr15:39747600-39748800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:39747600-39748800	Enhancers	Stomach Mucosa	stomach

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