Variant report

Variant	rs17643920
Chromosome Location	chr15:40040523-40040524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40040436-40040860	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr15:40040517-40040897	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr15:40040520-40040881	A549	lung:	n/a	n/a
4	HDAC2	chr15:40040505-40040827	MCF-7	breast:	n/a	n/a
5	TFAP2C	chr15:40040475-40040868	Hela-S3	cervix:	n/a	chr15:40040704-40040719
6	FOS	chr15:40040518-40040845	MCF10A-Er-Src	breast:	n/a	n/a
7	NR2F2	chr15:40040520-40040895	MCF-7	breast:	n/a	n/a
8	NR2F2	chr15:40040467-40040937	MCF-7	breast:	n/a	n/a
9	CEBPB	chr15:40040393-40040981	A549	lung:	n/a	n/a
10	STAT3	chr15:40040518-40040857	MCF10A-Er-Src	breast:	n/a	n/a
11	NR3C1	chr15:40040486-40040772	A549	lung:	n/a	n/a
12	FOS	chr15:40040515-40040860	MCF10A-Er-Src	breast:	n/a	n/a
13	REST	chr15:40040454-40040914	A549	lung:	n/a	n/a
14	EP300	chr15:40040383-40040882	A549	lung:	n/a	n/a
15	MYC	chr15:40040496-40040836	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF12	chr15:40040222-40040983	A549	lung:	n/a	n/a
17	FOS	chr15:40040497-40040848	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr15:40040369-40040868	A549	lung:	n/a	n/a
19	FOXA1	chr15:40040352-40040851	A549	lung:	n/a	n/a
20	MYC	chr15:40040484-40040846	MCF10A-Er-Src	breast:	n/a	n/a
21	TFAP2A	chr15:40040472-40040876	Hela-S3	cervix:	n/a	chr15:40040622-40040637
22	RCOR1	chr15:40040519-40040869	Hela-S3	cervix:	n/a	n/a
23	NR3C1	chr15:40040453-40040831	A549	lung:	n/a	n/a
24	EP300	chr15:40040489-40040857	Hela-S3	cervix:	n/a	n/a
25	NR3C1	chr15:40040416-40040907	A549	lung:	n/a	n/a
26	SP1	chr15:40040365-40040946	A549	lung:	n/a	n/a
27	STAT3	chr15:40040343-40040846	MCF10A-Er-Src	breast:	n/a	n/a
28	SP1	chr15:40040385-40040969	A549	lung:	n/a	n/a
29	BCL3	chr15:40040414-40040925	A549	lung:	n/a	n/a
30	CEBPB	chr15:40040483-40040904	Hela-S3	cervix:	n/a	n/a
31	NR3C1	chr15:40040413-40040829	A549	lung:	n/a	n/a

Variant related genes	Relation type
FSIP1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10520151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1166717	0.82[EUR][1000 genomes]
rs12899969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12903306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907894	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916159	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491624	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2171311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576930	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34047703	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34185057	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34439198	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34937456	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35273063	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35652496	0.82[EUR][1000 genomes]
rs35898600	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4115216	0.86[CEU][hapmap]
rs4924386	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62004778	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40035600-40050000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40037800-40041400	Enhancers	Hela-S3	cervix
3	chr15:40038400-40040800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:40038400-40041200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:40038400-40041200	Enhancers	Osteobl	bone
6	chr15:40038600-40041200	Enhancers	NHDF-Ad	bronchial
7	chr15:40039200-40041000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr15:40039400-40040800	Enhancers	NHEK	skin
9	chr15:40039400-40049000	Weak transcription	HUVEC	blood vessel
10	chr15:40039600-40040800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:40039800-40041000	Enhancers	Rectal Smooth Muscle	rectum
12	chr15:40040000-40040800	Enhancers	HMEC	breast
13	chr15:40040200-40040800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr15:40040200-40040800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:40040200-40040800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr15:40040200-40041000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:40040200-40041000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:40040400-40040800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:40040400-40040800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:40040400-40040800	Active TSS	A549	lung
21	chr15:40040400-40041000	Enhancers	Adipose Nuclei	Adipose

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