Variant report

Variant	rs12693184
Chromosome Location	chr2:180137539-180137540
allele	A/C
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	GATA3	chr2:180136874-180137671	A549	lung:	n/a	chr2:180137275-180137282
2	KAP1	chr2:180137056-180137926	U2OS	brain:	n/a	chr2:180137135-180137143
3	TBP	chr2:180137156-180137795	HepG2	liver:	n/a	n/a
4	HEY1	chr2:180137178-180137740	HepG2	liver:	n/a	n/a
5	RFX5	chr2:180137024-180138055	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr2:180137093-180137995	Hela-S3	cervix:	n/a	n/a
7	RXRA	chr2:180137056-180137705	HepG2	liver:	n/a	chr2:180137283-180137299 chr2:180137289-180137298
8	EP300	chr2:180137009-180138032	HepG2	liver:	n/a	chr2:180137800-180137807 chr2:180137427-180137441
9	MAX	chr2:180137086-180137980	Hela-S3	cervix:	n/a	n/a
10	USF2	chr2:180137533-180137821	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr2:180137206-180138010	Hela-S3	cervix:	n/a	n/a
12	NFIC	chr2:180137004-180137898	SK-N-SH	brain:	n/a	n/a
13	CEBPB	chr2:180137423-180137927	HepG2	liver:	n/a	chr2:180137601-180137614
14	FOXA2	chr2:180136874-180137808	A549	lung:	n/a	n/a
15	MBD4	chr2:180136817-180138430	HepG2	liver:	n/a	n/a
16	FOS	chr2:180137017-180138027	MCF10A-Er-Src	breast:	n/a	chr2:180137196-180137208
17	FOXA2	chr2:180136778-180138066	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:180137474-180137766	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:180136950-180138083	MCF10A-Er-Src	breast:	n/a	n/a
20	NR2F2	chr2:180137039-180137596	MCF-7	breast:	n/a	n/a
21	ARID3A	chr2:180136821-180137690	HepG2	liver:	n/a	n/a
22	NFIC	chr2:180137069-180137835	HepG2	liver:	n/a	n/a
23	FOSL2	chr2:180136953-180137545	A549	lung:	n/a	chr2:180137196-180137208
24	GATA3	chr2:180137078-180137785	MCF-7	breast:	n/a	chr2:180137275-180137282
25	FOXA1	chr2:180136934-180137813	HepG2	liver:	n/a	n/a
26	GTF2F1	chr2:180137215-180137932	Hela-S3	cervix:	n/a	n/a
27	STAT3	chr2:180137320-180138027	MCF10A-Er-Src	breast:	n/a	n/a
28	FOXA1	chr2:180137055-180137825	HepG2	liver:	n/a	n/a
29	FOXA2	chr2:180137023-180137673	HepG2	liver:	n/a	n/a
30	HDAC2	chr2:180137043-180137701	HepG2	liver:	n/a	chr2:180137426-180137440 chr2:180137427-180137441
31	HEY1	chr2:180137107-180137726	HepG2	liver:	n/a	n/a
32	MYBL2	chr2:180136857-180137954	HepG2	liver:	n/a	n/a
33	MXI1	chr2:180137170-180137613	HepG2	liver:	n/a	n/a
34	EP300	chr2:180136813-180137649	HepG2	liver:	n/a	chr2:180137427-180137441
35	STAT3	chr2:180137149-180137965	MCF10A-Er-Src	breast:	n/a	n/a
36	BHLHE40	chr2:180137156-180137744	HepG2	liver:	n/a	n/a
37	GATA2	chr2:180137123-180137736	HUVEC	blood vessel:	n/a	chr2:180137275-180137282
38	GATA3	chr2:180136820-180137768	MCF-7	breast:	n/a	chr2:180137275-180137282
39	CEBPB	chr2:180137512-180137916	A549	lung:	n/a	chr2:180137601-180137614
40	POLR2A	chr2:180137214-180138930	HepG2	liver:	n/a	n/a
41	JUND	chr2:180137058-180137785	HepG2	liver:	n/a	chr2:180137196-180137208
42	TCF12	chr2:180136993-180137618	SK-N-SH	brain:	n/a	chr2:180137531-180137541
43	FOXA1	chr2:180136946-180137954	HepG2	liver:	n/a	n/a
44	YY1	chr2:180137383-180137720	HepG2	liver:	n/a	n/a
45	SMC3	chr2:180137177-180137976	Hela-S3	cervix:	n/a	n/a
46	MYBL2	chr2:180137021-180137816	HepG2	liver:	n/a	n/a
47	SP1	chr2:180137028-180137549	A549	lung:	n/a	chr2:180137176-180137185
48	FOXA1	chr2:180137024-180137786	HepG2	liver:	n/a	n/a
49	TCF7L2	chr2:180137109-180137955	Hela-S3	cervix:	n/a	n/a
50	MYC	chr2:180137085-180137992	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237477	TF binding region
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10172996	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1159257	0.89[YRI][hapmap];0.83[AFR][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	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180138000	Weak transcription	Gastric	stomach
2	chr2:180130000-180138200	Weak transcription	Aorta	Aorta
3	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:180130400-180138400	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:180130600-180138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:180133600-180138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:180133600-180138800	Weak transcription	Placenta	Placenta
10	chr2:180133600-180140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:180133800-180138800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:180133800-180138800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:180133800-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:180133800-180141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:180134000-180139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:180134000-180142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:180135000-180138200	Enhancers	Brain Hippocampus Middle	brain
18	chr2:180135200-180140400	Enhancers	Brain Angular Gyrus	brain
19	chr2:180135400-180140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:180136200-180137600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:180136200-180137600	Enhancers	Stomach Mucosa	stomach
22	chr2:180136200-180138200	Enhancers	HUVEC	blood vessel
23	chr2:180136200-180138200	Enhancers	NHEK	skin
24	chr2:180136400-180137800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:180136600-180137800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:180136600-180141000	Weak transcription	Esophagus	oesophagus
27	chr2:180136800-180137800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:180136800-180138000	Enhancers	Liver	Liver
29	chr2:180136800-180138800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:180137000-180137600	Enhancers	Stomach Smooth Muscle	stomach
31	chr2:180137000-180137800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr2:180137000-180138000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:180137000-180139000	Flanking Active TSS	HepG2	liver
34	chr2:180137000-180139600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:180137000-180140600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr2:180137200-180137600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:180137200-180137600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:180137200-180137600	Flanking Active TSS	A549	lung
39	chr2:180137200-180137800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:180137200-180137800	Enhancers	Fetal Kidney	kidney
41	chr2:180137200-180137800	Enhancers	NH-A	brain
42	chr2:180137200-180137800	Enhancers	NHDF-Ad	bronchial
43	chr2:180137200-180137800	Flanking Active TSS	Osteobl	bone
44	chr2:180137200-180138000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:180137200-180138000	Enhancers	Fetal Intestine Small	intestine
46	chr2:180137200-180138200	Flanking Active TSS	Hela-S3	cervix
47	chr2:180137200-180138600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:180137200-180138800	Enhancers	Fetal Lung	lung
49	chr2:180137200-180140000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:180137200-180141200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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