Variant report

Variant	rs12439767
Chromosome Location	chr15:93463855-93463856
allele	C/G
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	chr15:93463603-93465528	K562	blood:	n/a	n/a
2	POLR2A	chr15:93463583-93466834	K562	blood:	n/a	n/a
3	POLR2A	chr15:93463656-93464327	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr15:93463691-93465348	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr15:93463784-93465404	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr15:93463568-93466760	U87	brain:	n/a	n/a
7	POLR2A	chr15:93463008-93472730	K562	blood:	n/a	n/a
8	POLR2A	chr15:93463684-93466928	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:93463762-93464552	U87	brain:	n/a	n/a
10	POLR2A	chr15:93463573-93465288	GM12878	blood:	n/a	n/a
11	MAFF	chr15:93463685-93464308	K562	blood:	n/a	chr15:93464097-93464115
12	POLR2A	chr15:93462946-93466287	A549	lung:	n/a	n/a
13	TCF7L2	chr15:93463759-93464182	PANC-1	pancreas:	n/a	chr15:93464011-93464018 chr15:93464086-93464102 chr15:93464087-93464101 chr15:93464088-93464098 chr15:93464089-93464098 chr15:93464090-93464099 chr15:93464086-93464102
14	POLR2A	chr15:93462854-93466503	HepG2	liver:	n/a	n/a
15	POLR2A	chr15:93463719-93464330	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
2	chr15:93347226..93350141-chr15:93462968..93465327,2	MCF-7	breast:
3	chr15:93360172..93364704-chr15:93459982..93465049,6	MCF-7	breast:
4	chr15:93345806..93348640-chr15:93462884..93464595,2	K562	blood:
5	chr15:93463262..93465230-chr15:93468771..93470893,2	K562	blood:
6	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:
7	chr15:93459868..93463900-chr15:93464643..93468863,9	K562	blood:
8	chr15:93347140..93350047-chr15:93463095..93464830,2	K562	blood:
9	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:
10	chr15:93461610..93464401-chr15:93531914..93533700,2	K562	blood:
11	chr15:93351614..93354047-chr15:93463305..93465417,2	K562	blood:

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000173575	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2272452	1.00[AFR][1000 genomes]
rs4411466	1.00[AFR][1000 genomes]
rs4778050	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93451800-93464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:93454000-93464000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:93455600-93464400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:93455600-93464800	Weak transcription	Fetal Brain Female	brain
5	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:93457200-93464000	Weak transcription	Gastric	stomach
7	chr15:93457800-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:93460000-93464000	Weak transcription	Right Ventricle	heart
9	chr15:93460000-93464200	Weak transcription	Esophagus	oesophagus
10	chr15:93460000-93464200	Weak transcription	Spleen	Spleen
11	chr15:93460600-93466400	Genic enhancers	Fetal Intestine Small	intestine
12	chr15:93460800-93464000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:93460800-93464000	Weak transcription	Pancreas	Pancrea
14	chr15:93460800-93464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:93460800-93464400	Weak transcription	Lung	lung
16	chr15:93461000-93464000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:93461200-93464000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:93461200-93464000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:93461200-93464000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:93461200-93464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:93461200-93464200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:93461200-93464800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:93461200-93465600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:93461200-93465600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:93461200-93465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr15:93461200-93466600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr15:93461200-93467200	Enhancers	Stomach Mucosa	stomach
28	chr15:93461200-93467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr15:93461200-93467600	Weak transcription	Fetal Brain Male	brain
30	chr15:93461200-93467600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:93461400-93464000	Weak transcription	Placenta	Placenta
33	chr15:93461400-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:93461400-93464400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:93461600-93464200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:93461600-93464200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:93461600-93464200	Weak transcription	Right Atrium	heart
38	chr15:93461600-93464200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:93461600-93464400	Weak transcription	Thymus	Thymus
40	chr15:93461600-93466000	Enhancers	Liver	Liver
41	chr15:93461600-93467600	Enhancers	Brain Cingulate Gyrus	brain
42	chr15:93461600-93471600	Weak transcription	Ovary	ovary
43	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:93461800-93464200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:93461800-93464400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:93461800-93464800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:93462000-93464400	Weak transcription	Fetal Kidney	kidney
49	chr15:93462000-93464800	Enhancers	Stomach Smooth Muscle	stomach
50	chr15:93462000-93465600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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