Variant report

Variant	rs12595447
Chromosome Location	chr15:49914716-49914717
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	chr15:49911978-49916148	MCF10A-Er-Src	breast:	n/a	n/a
2	TBL1XR1	chr15:49914634-49914749	GM12878	blood:	n/a	n/a
3	CTCF	chr15:49914640-49914790	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:49912243-49914793	Hela-S3	cervix:	n/a	n/a
5	MYC	chr15:49914651-49914751	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr15:49914668-49915233	MCF-7	breast:	n/a	chr15:49914951-49914969 chr15:49914954-49914967
7	MXI1	chr15:49911990-49915525	SK-N-SH	brain:	n/a	n/a
8	CHD1	chr15:49912216-49914778	IMR90	lung:	n/a	n/a
9	HCFC1	chr15:49911005-49914797	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr15:49912336-49914954	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr15:49914695-49915239	MCF-7	breast:	n/a	chr15:49914951-49914969 chr15:49914954-49914967
12	POLR2A	chr15:49912375-49916243	ProgFib	skin:	n/a	n/a
13	POLR2A	chr15:49911535-49916197	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:49914042..49915068-chr15:50194363..50195235,4	MCF-7	breast:
2	chr15:49914708..49917210-chr15:49937827..49939413,2	MCF-7	breast:
3	chr15:49914376..49915416-chr15:50124445..50125402,4	MCF-7	breast:
4	chr15:49914595..49915377-chr15:50124565..50125477,5	MCF-7	breast:
5	chr15:49913369..49915097-chr15:49925373..49927473,2	MCF-7	breast:
6	chr14:25147349..25148317-chr15:49914642..49915614,2	MCF-7	breast:
7	chr15:49913331..49915025-chr17:60882380..60884331,2	MCF-7	breast:

Variant related genes	Relation type
FAM227B	TF binding region
ENSG00000173838	Chromatin interaction
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12591533	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594585	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17482833	0.87[ASN][1000 genomes]
rs34833569	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57496745	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58275754	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59589271	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729121	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72729125	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72729127	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729130	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72729132	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729174	0.86[EUR][1000 genomes]
rs72729189	0.86[EUR][1000 genomes]
rs72729199	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72731108	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72731119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72731121	0.88[EUR][1000 genomes]
rs72731122	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72731124	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72731125	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72731137	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72731140	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49911400-49916000	Active TSS	Stomach Smooth Muscle	stomach
2	chr15:49911600-49916600	Active TSS	GM12878-XiMat	blood
3	chr15:49911800-49914800	Active TSS	K562	blood
4	chr15:49911800-49915200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:49912000-49915000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr15:49912200-49914800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:49912200-49914800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:49912200-49914800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:49912200-49914800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:49912200-49914800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:49912400-49914800	Active TSS	NHLF	lung
12	chr15:49912400-49915200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:49912600-49915800	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr15:49912800-49915000	Active TSS	Pancreas	Pancrea
15	chr15:49913600-49915000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr15:49913600-49916600	Flanking Active TSS	Osteobl	bone
17	chr15:49913600-49937400	Weak transcription	Spleen	Spleen
18	chr15:49913800-49914800	Flanking Active TSS	Fetal Heart	heart
19	chr15:49913800-49914800	Flanking Active TSS	Fetal Lung	lung
20	chr15:49913800-49914800	Flanking Active TSS	Dnd41	blood
21	chr15:49913800-49916200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:49913800-49916600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:49914000-49915000	Enhancers	Primary B cells from peripheral blood	blood
24	chr15:49914000-49915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:49914000-49915600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:49914000-49915600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:49914000-49917000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:49914000-49917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:49914000-49917800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:49914000-49917800	Weak transcription	Esophagus	oesophagus
31	chr15:49914000-49917800	Weak transcription	Left Ventricle	heart
32	chr15:49914000-49917800	Weak transcription	Lung	lung
33	chr15:49914000-49930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:49914200-49914800	Enhancers	Primary B cells from cord blood	blood
35	chr15:49914200-49914800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr15:49914200-49914800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr15:49914200-49914800	Flanking Active TSS	HMEC	breast
38	chr15:49914200-49915000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr15:49914200-49915000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr15:49914200-49915000	Enhancers	Fetal Thymus	thymus
41	chr15:49914200-49915400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr15:49914200-49916200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:49914200-49916200	Flanking Active TSS	NHDF-Ad	bronchial
44	chr15:49914200-49916600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:49914400-49914800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr15:49914400-49914800	Enhancers	Brain Anterior Caudate	brain
47	chr15:49914400-49914800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr15:49914400-49915000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:49914400-49915000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr15:49914400-49915200	Enhancers	Brain Angular Gyrus	brain

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