Variant report

Variant	rs2870937
Chromosome Location	chr12:67819682-67819683
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	NFIC	chr12:67819552-67820446	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr12:67819644-67820638	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr12:67819525-67820435	ECC-1	luminal epithelium:	n/a	n/a
4	SETDB1	chr12:67819556-67820348	U2OS	brain:	n/a	n/a
5	USF1	chr12:67819682-67820194	SK-N-SH_RA	brain:	n/a	chr12:67819961-67819972
6	POLR2A	chr12:67819658-67820206	SK-N-MC	brain:	n/a	n/a
7	USF1	chr12:67819597-67820323	ECC-1	luminal epithelium:	n/a	chr12:67819961-67819972
8	FOXM1	chr12:67819604-67820600	ECC-1	luminal epithelium:	n/a	n/a
9	FOXM1	chr12:67819642-67820430	ECC-1	luminal epithelium:	n/a	n/a
10	E2F4	chr12:67819592-67819871	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr12:67819679-67820582	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr12:67819562-67820327	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr12:67819495-67820660	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr12:67819644-67820596	SK-N-SH	brain:	n/a	n/a
15	MAX	chr12:67819562-67820416	ECC-1	luminal epithelium:	n/a	n/a
16	KAP1	chr12:67819404-67820453	HEK293	kidney:	n/a	n/a
17	KAP1	chr12:67819495-67820473	U2OS	brain:	n/a	n/a
18	MAX	chr12:67819495-67820734	ECC-1	luminal epithelium:	n/a	n/a
19	USF1	chr12:67819675-67820286	ECC-1	luminal epithelium:	n/a	chr12:67819961-67819972

Variant related genes	Relation type
NTAN1P3	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10506549	0.82[JPT][hapmap]
rs10878616	0.82[JPT][hapmap]
rs11176739	0.82[JPT][hapmap]
rs12828359	0.82[JPT][hapmap]
rs1882033	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs1882280	0.82[JPT][hapmap]
rs1920430	0.82[JPT][hapmap]
rs4913247	0.82[JPT][hapmap]
rs4913248	0.82[JPT][hapmap]
rs4913249	0.82[JPT][hapmap]
rs4913323	0.82[JPT][hapmap]
rs4913324	0.82[JPT][hapmap]
rs7132301	0.82[JPT][hapmap]

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	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2870937	TBK1	cis	cerebellum	SCAN
rs2870937	IFNG	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67809200-67819800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:67809200-67824000	Weak transcription	Psoas Muscle	Psoas
3	chr12:67810200-67819800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:67810600-67819800	Weak transcription	HSMMtube	muscle
5	chr12:67814400-67819800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:67814600-67819800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:67814600-67819800	Weak transcription	Fetal Lung	lung
8	chr12:67814800-67819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:67817800-67830600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:67818600-67820000	Enhancers	HMEC	breast
11	chr12:67818600-67821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:67818600-67821000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:67818600-67822400	Enhancers	Stomach Mucosa	stomach
14	chr12:67818600-67823000	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:67818600-67827000	Enhancers	Fetal Intestine Small	intestine
16	chr12:67818600-67832000	Enhancers	Fetal Intestine Large	intestine
17	chr12:67818800-67819800	Weak transcription	Fetal Stomach	stomach
18	chr12:67818800-67820200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr12:67818800-67820600	Enhancers	NHDF-Ad	bronchial
20	chr12:67818800-67821200	Weak transcription	Colonic Mucosa	Colon
21	chr12:67818800-67823000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:67819000-67820200	Weak transcription	Small Intestine	intestine
23	chr12:67819000-67821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:67819000-67821400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:67819000-67821800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:67819400-67820200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr12:67819400-67820600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:67819400-67820600	Enhancers	Fetal Heart	heart
29	chr12:67819400-67821400	Weak transcription	NHEK	skin
30	chr12:67819600-67819800	Enhancers	NH-A	brain
31	chr12:67819600-67820000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:67819600-67820000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr12:67819600-67820000	Enhancers	Pancreas	Pancrea
34	chr12:67819600-67820200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:67819600-67820200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:67819600-67820600	Enhancers	Fetal Kidney	kidney
37	chr12:67819600-67820600	Enhancers	GM12878-XiMat	blood
38	chr12:67819600-67822000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:67819600-67822200	Weak transcription	Placenta	Placenta
40	chr12:67819600-67825400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:67819600-67831400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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