Variant report

Variant	rs12997583
Chromosome Location	chr2:187351346-187351347
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	EGR1	chr2:187350632-187351680	MCF-7	breast:	n/a	chr2:187351399-187351409 chr2:187350888-187350897 chr2:187351398-187351411 chr2:187351371-187351384 chr2:187351397-187351411 chr2:187351371-187351384 chr2:187351371-187351384 chr2:187351366-187351388 chr2:187350887-187350896
2	CHD2	chr2:187350248-187351748	GM12878	blood:	n/a	n/a
3	MYC	chr2:187350427-187351642	K562	blood:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
4	POLR2A	chr2:187350232-187351464	Hela-S3	cervix:	n/a	n/a
5	EBF1	chr2:187351164-187351694	GM12878	blood:	n/a	n/a
6	SMARCB1	chr2:187350474-187351564	Hela-S3	cervix:	n/a	n/a
7	SP1	chr2:187350458-187351623	GM12878	blood:	n/a	chr2:187351194-187351206 chr2:187351195-187351209 chr2:187350856-187350870 chr2:187351194-187351206 chr2:187351196-187351205 chr2:187350856-187350865 chr2:187351195-187351205
8	POLR2A	chr2:187350375-187351352	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr2:187349993-187352088	MCF10A-Er-Src	breast:	n/a	n/a
10	ZMIZ1	chr2:187350379-187351964	K562	blood:	n/a	n/a
11	SIN3A	chr2:187350487-187351488	GM12878	blood:	n/a	chr2:187350890-187350903
12	ELF1	chr2:187350481-187351363	HepG2	liver:	n/a	chr2:187350904-187350913 chr2:187350903-187350912
13	TAF1	chr2:187350443-187351523	ECC-1	luminal epithelium:	n/a	n/a
14	CREB1	chr2:187350368-187351632	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:187350375-187351660	K562	blood:	n/a	n/a
16	MXI1	chr2:187349908-187352518	SK-N-SH	brain:	n/a	n/a
17	SPI1	chr2:187350531-187351479	HL-60	blood:	n/a	chr2:187350729-187350736 chr2:187351233-187351246 chr2:187350857-187350870
18	POLR2A	chr2:187349863-187352422	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr2:187350059-187352376	K562	blood:	n/a	n/a
20	POLR2A	chr2:187350428-187351544	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF143	chr2:187350535-187351505	H1-hESC	embryonic stem cell:	n/a	chr2:187350926-187350941
22	CUX1	chr2:187350550-187351569	GM12878	blood:	n/a	n/a
23	TBP	chr2:187350373-187351691	H1-hESC	embryonic stem cell:	n/a	n/a
24	HDAC2	chr2:187350351-187351550	HepG2	liver:	n/a	chr2:187350408-187350417 chr2:187350887-187350896
25	TAF1	chr2:187350479-187351355	MCF-7	breast:	n/a	n/a
26	MAFK	chr2:187350573-187351500	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr2:187350289-187351699	U87	brain:	n/a	n/a
28	MBD4	chr2:187349546-187351735	HepG2	liver:	n/a	n/a
29	E2F6	chr2:187350325-187351564	H1-hESC	embryonic stem cell:	n/a	chr2:187351368-187351378 chr2:187350888-187350897 chr2:187350840-187350851
30	POLR2A	chr2:187350403-187351522	MCF-7	breast:	n/a	n/a
31	MYC	chr2:187349894-187351872	A549	lung:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
32	POLR2A	chr2:187350388-187351717	K562	blood:	n/a	n/a
33	HNF4G	chr2:187350547-187351353	HepG2	liver:	n/a	n/a
34	HEY1	chr2:187349947-187351663	HepG2	liver:	n/a	n/a
35	ETS1	chr2:187350618-187351400	K562	blood:	n/a	chr2:187350901-187350912 chr2:187350726-187350741 chr2:187351196-187351207 chr2:187350857-187350868 chr2:187350901-187350911
36	USF1	chr2:187351109-187351421	SK-N-SH_RA	brain:	n/a	n/a
37	CREB1	chr2:187349971-187352009	K562	blood:	n/a	n/a
38	POLR2A	chr2:187350270-187351579	MCF-7	breast:	n/a	n/a
39	EP300	chr2:187350454-187351366	A549	lung:	n/a	n/a
40	MXI1	chr2:187350277-187352022	HepG2	liver:	n/a	n/a
41	MYC	chr2:187350492-187351466	HUVEC	blood vessel:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
42	BCL3	chr2:187350458-187351513	GM12878	blood:	n/a	chr2:187351376-187351389
43	MBD4	chr2:187349952-187351605	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:187350419-187351616	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:187350502-187351448	GM10847	blood:	n/a	n/a
46	POLR2A	chr2:187349962-187351739	Hela-S3	cervix:	n/a	n/a
47	MAX	chr2:187350371-187351674	K562	blood:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
48	YY1	chr2:187350473-187351427	ECC-1	luminal epithelium:	n/a	chr2:187351194-187351205
49	TAF1	chr2:187350335-187351564	GM12891	blood:	n/a	n/a
50	ATF3	chr2:187350639-187351480	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:187349672..187352615-chr2:187454696..187458504,4	K562	blood:
2	chr2:187350319..187353074-chr2:187452754..187457832,8	K562	blood:
3	chr2:187350070..187352270-chr2:187452591..187455868,3	MCF-7	breast:
4	chr2:187350930..187352982-chr2:187364915..187367637,2	MCF-7	breast:
5	chr2:187350028..187353171-chr2:187452977..187457092,6	MCF-7	breast:

Variant related genes	Relation type
ZC3H15	TF binding region
ENSG00000138448	Chromatin interaction
ENSG00000268846	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10210844	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1026118	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12473076	0.95[JPT][hapmap]
rs12993773	0.95[JPT][hapmap]
rs12999247	0.95[JPT][hapmap]
rs13025505	0.95[JPT][hapmap]
rs1349154	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1448854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1451874	0.95[JPT][hapmap]
rs1562646	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2044919	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs2119861	0.82[CEU][hapmap]
rs2119865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2305409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3768775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3768776	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4144785	0.91[JPT][hapmap]
rs4666705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4667100	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4667102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6434177	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs6434179	0.95[JPT][hapmap]
rs6434182	0.95[JPT][hapmap]
rs6434183	0.95[JPT][hapmap]
rs6712627	0.95[JPT][hapmap]
rs6717081	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6740632	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7562659	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7568700	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7581081	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs7586276	0.95[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr2:187348200-187352200	Active TSS	Colonic Mucosa	Colon
2	chr2:187348200-187353400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr2:187348600-187352600	Active TSS	Fetal Intestine Small	intestine
4	chr2:187348600-187353000	Active TSS	Fetal Intestine Large	intestine
5	chr2:187348800-187352200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr2:187348800-187353200	Active TSS	K562	blood
7	chr2:187349000-187352800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:187349000-187353200	Active TSS	GM12878-XiMat	blood
9	chr2:187349000-187354000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:187349200-187352200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:187349400-187352000	Active TSS	Fetal Kidney	kidney
12	chr2:187349400-187353800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:187349600-187352000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:187349600-187352000	Active TSS	Muscle Satellite Cultured Cells	--
15	chr2:187349600-187352000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:187349600-187352200	Bivalent/Poised TSS	HepG2	liver
17	chr2:187349600-187352600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:187349600-187353200	Active TSS	Psoas Muscle	Psoas
19	chr2:187349800-187352200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:187349800-187352200	Active TSS	NHDF-Ad	bronchial
21	chr2:187349800-187352400	Active TSS	A549	lung
22	chr2:187349800-187352600	Active TSS	HSMMtube	muscle
23	chr2:187349800-187352600	Active TSS	NHEK	skin
24	chr2:187349800-187353000	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr2:187349800-187353200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:187349800-187353200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:187349800-187353200	Active TSS	HMEC	breast
28	chr2:187349800-187353400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:187350000-187351600	Active TSS	Brain Cingulate Gyrus	brain
30	chr2:187350000-187351800	Active TSS	Primary T cells fromperipheralblood	blood
31	chr2:187350000-187351800	Active TSS	Liver	Liver
32	chr2:187350000-187351800	Active TSS	Fetal Brain Male	brain
33	chr2:187350000-187351800	Active TSS	Fetal Lung	lung
34	chr2:187350000-187351800	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:187350000-187352000	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr2:187350000-187352000	Active TSS	Brain Germinal Matrix	brain
37	chr2:187350000-187352000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:187350000-187352000	Active TSS	Colon Smooth Muscle	Colon
39	chr2:187350000-187352000	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr2:187350000-187352000	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:187350000-187352200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr2:187350000-187352200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:187350000-187352200	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr2:187350000-187352200	Active TSS	Left Ventricle	heart
45	chr2:187350000-187352200	Active TSS	Osteobl	bone
46	chr2:187350000-187352400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr2:187350000-187352400	Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:187350000-187352400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr2:187350000-187352400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:187350000-187352400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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