Variant report

Variant	rs12438465
Chromosome Location	chr15:39745561-39745562
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:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11070204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1158918	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11633970	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857561	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593294	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	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1812583	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1947782	0.82[ASN][1000 genomes]
rs1993892	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1993893	0.89[ASN][1000 genomes]
rs2086166	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2127029	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2411293	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34329697	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4244571	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4486853	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924361	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924363	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59431794	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60697424	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7171244	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7180041	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7350779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74008200	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74010438	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8030260	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032900	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs8033214	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9888722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920539	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	esv3419623	chr15:39742460-39746758	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3310891	chr15:39743285-39746233	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3528510	chr15:39743685-39745883	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv569224	chr15:39744272-39748158	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv511556	chr15:39744272-39748389	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv569226	chr15:39744425-39748158	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	chr15:39727200-39746800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr15:39740000-39759400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:39740400-39747200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:39743000-39745600	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:39743800-39745600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:39744000-39747600	Weak transcription	NHLF	lung
7	chr15:39744200-39745600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:39744200-39745600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:39744200-39745600	Weak transcription	NHDF-Ad	bronchial
10	chr15:39744400-39748400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:39744600-39745800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:39744600-39753400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:39745200-39745600	Enhancers	Colon Smooth Muscle	Colon
14	chr15:39745200-39746600	Enhancers	Fetal Stomach	stomach
15	chr15:39745200-39747400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:39745400-39745600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:39745400-39745600	Enhancers	GM12878-XiMat	blood
18	chr15:39745400-39745800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:39745400-39746200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr15:39745400-39746800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr15:39745400-39746800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:39745400-39747400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr15:39745400-39747800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr15:39745400-39748800	Enhancers	Osteobl	bone
25	chr15:39745400-39749600	Enhancers	Fetal Lung	lung

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