Variant report

Variant	rs4887003
Chromosome Location	chr15:78370775-78370776
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	HCFC1	chr15:78368897-78370952	Hela-S3	cervix:	n/a	n/a
2	MAZ	chr15:78368980-78371018	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1053506	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11072726	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11633329	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11633569	1.00[ASN][1000 genomes]
rs11636889	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12595595	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12898535	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12900731	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12901492	1.00[ASN][1000 genomes]
rs12913206	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12915731	1.00[JPT][hapmap]
rs12915847	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12916320	1.00[ASN][1000 genomes]
rs1348256	1.00[ASN][1000 genomes]
rs1837911	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1837912	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2015951	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2867984	1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4316722	1.00[ASW][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4411474	1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	1.00[ASN][1000 genomes]
rs4886556	1.00[ASN][1000 genomes]
rs4886985	1.00[ASN][1000 genomes]
rs4886986	1.00[ASN][1000 genomes]
rs4886987	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4886993	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4886997	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4886998	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887001	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887002	1.00[ASN][1000 genomes]
rs4887004	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61732053	1.00[ASN][1000 genomes]
rs7163997	1.00[ASN][1000 genomes]
rs7169882	1.00[ASN][1000 genomes]
rs7170101	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7170286	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7170452	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7173128	0.83[ASW][hapmap]
rs7175192	1.00[ASN][1000 genomes]
rs7175235	1.00[ASN][1000 genomes]
rs7175975	1.00[ASN][1000 genomes]
rs7180684	1.00[JPT][hapmap]
rs8025423	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8033216	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs894295	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs894296	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs894302	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9788640	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9920180	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78368800-78370800	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr15:78369000-78370800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:78369200-78370800	Active TSS	Brain Anterior Caudate	brain
4	chr15:78369200-78370800	Active TSS	A549	lung
5	chr15:78370000-78372400	Weak transcription	Spleen	Spleen
6	chr15:78370200-78370800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr15:78370200-78370800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr15:78370200-78370800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:78370200-78370800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:78370200-78370800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr15:78370400-78370800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:78370400-78370800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:78370400-78370800	Enhancers	Liver	Liver
14	chr15:78370400-78370800	Enhancers	Fetal Thymus	thymus
15	chr15:78370400-78370800	Flanking Active TSS	HepG2	liver
16	chr15:78370400-78370800	Enhancers	HSMM	muscle
17	chr15:78370400-78371800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:78370400-78372200	Weak transcription	Ovary	ovary
19	chr15:78370400-78372200	Weak transcription	Pancreas	Pancrea
20	chr15:78370400-78373600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:78370400-78374000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:78370400-78374200	Weak transcription	Colonic Mucosa	Colon
23	chr15:78370400-78374800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:78370400-78374800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:78370400-78374800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:78370400-78375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:78370400-78375000	Weak transcription	Gastric	stomach
28	chr15:78370400-78375000	Weak transcription	Lung	lung
29	chr15:78370400-78375000	Weak transcription	Small Intestine	intestine
30	chr15:78370400-78375600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:78370400-78376600	Weak transcription	Right Atrium	heart
32	chr15:78370400-78377000	Weak transcription	Esophagus	oesophagus
33	chr15:78370600-78370800	Enhancers	Primary B cells from peripheral blood	blood
34	chr15:78370600-78370800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr15:78370600-78370800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr15:78370600-78370800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:78370600-78370800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr15:78370600-78370800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:78370600-78370800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:78370600-78370800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:78370600-78370800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr15:78370600-78370800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr15:78370600-78370800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:78370600-78370800	Enhancers	Brain Cingulate Gyrus	brain
45	chr15:78370600-78370800	Enhancers	Brain Hippocampus Middle	brain
46	chr15:78370600-78370800	Enhancers	Colon Smooth Muscle	Colon
47	chr15:78370600-78370800	Enhancers	Duodenum Mucosa	Duodenum
48	chr15:78370600-78370800	Active TSS	Fetal Brain Male	brain
49	chr15:78370600-78370800	Enhancers	Fetal Intestine Large	intestine
50	chr15:78370600-78370800	Enhancers	Fetal Intestine Small	intestine

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