Variant report

Variant	rs11694920
Chromosome Location	chr2:55450484-55450485
allele	A/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	TAF1	chr2:55450449-55450801	GM12891	blood:	n/a	n/a
2	CTCF	chr2:55450440-55450590	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr2:55450436-55450637	IMR90	lung:	n/a	n/a
4	POLR2A	chr2:55450384-55450970	HL-60	blood:	n/a	n/a
5	YY1	chr2:55450469-55450680	GM12892	blood:	n/a	n/a
6	EGR1	chr2:55450398-55450730	ECC-1	luminal epithelium:	n/a	chr2:55450564-55450578
7	RUNX3	chr2:55450275-55450890	GM12878	blood:	n/a	n/a
8	NRF1	chr2:55450473-55450708	H1-hESC	embryonic stem cell:	n/a	chr2:55450634-55450648
9	EGR1	chr2:55450420-55450689	H1-hESC	embryonic stem cell:	n/a	chr2:55450564-55450578
10	POLR2A	chr2:55450400-55450935	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr2:55450340-55450490	HMEC	breast:	n/a	n/a
12	STAT5A	chr2:55450392-55451021	GM12878	blood:	n/a	chr2:55450764-55450776
13	TAF1	chr2:55450472-55450778	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:55450417-55450921	GM12878	blood:	n/a	n/a
15	MAX	chr2:55450418-55451036	K562	blood:	n/a	n/a
16	CTCF	chr2:55450380-55450530	AG04450	lung:	n/a	n/a
17	POLR2A	chr2:55450339-55451044	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr2:55450483-55450690	GM12892	blood:	n/a	n/a
19	TAF1	chr2:55450414-55450937	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:55450357-55451457	PANC-1	pancreas:	n/a	n/a
21	MAX	chr2:55450482-55450829	GM12878	blood:	n/a	n/a
22	EGR1	chr2:55450430-55450699	GM12878	blood:	n/a	chr2:55450564-55450578
23	JUND	chr2:55450451-55451023	A549	lung:	n/a	n/a
24	MAX	chr2:55450410-55450920	MCF-7	breast:	n/a	n/a
25	POLR2A	chr2:55450462-55451068	GM18951	blood:	n/a	n/a
26	NRF1	chr2:55450403-55450781	GM12878	blood:	n/a	chr2:55450634-55450648
27	TAF1	chr2:55450477-55450974	H1-hESC	embryonic stem cell:	n/a	n/a
28	MXI1	chr2:55450332-55450774	GM12878	blood:	n/a	n/a
29	CTCF	chr2:55450457-55450686	Lung_OC	lung:	n/a	n/a
30	E2F6	chr2:55450403-55450784	A549	lung:	n/a	chr2:55450770-55450784 chr2:55450636-55450645
31	POLR2A	chr2:55450384-55450807	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr2:55450364-55451326	MCF-7	breast:	n/a	n/a
33	E2F6	chr2:55450484-55451617	K562	blood:	n/a	chr2:55450770-55450784 chr2:55450636-55450645
34	MAX	chr2:55450432-55450789	K562	blood:	n/a	n/a
35	MYC	chr2:55450429-55450927	K562	blood:	n/a	n/a
36	HMGN3	chr2:55450482-55450969	K562	blood:	n/a	n/a
37	POLR2A	chr2:55450438-55451023	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr2:55450439-55450858	Spleen_OC	spleen:	n/a	chr2:55450842-55450855
39	ZEB1	chr2:55450484-55450750	GM12878	blood:	n/a	n/a
40	HDAC2	chr2:55450431-55450805	MCF-7	breast:	n/a	n/a
41	PAX5	chr2:55450444-55451035	GM12892	blood:	n/a	n/a
42	CTCF	chr2:55450422-55450671	K562	blood:	n/a	n/a
43	IRF1	chr2:55450398-55450566	K562	blood:	n/a	chr2:55450479-55450491
44	POLR2A	chr2:55450389-55451022	HUVEC	blood vessel:	n/a	n/a
45	PML	chr2:55450461-55450998	K562	blood:	n/a	n/a
46	ELF1	chr2:55450454-55451068	GM12878	blood:	n/a	n/a
47	CTCF	chr2:55450375-55450784	GM12878	blood:	n/a	n/a
48	POLR2A	chr2:55450463-55450930	Raji	blood:	n/a	n/a
49	POLR2A	chr2:55450368-55451061	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr2:55450429-55451058	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55449257..55451239-chr2:55511673..55514610,2	MCF-7	breast:
2	chr2:55435664..55437797-chr2:55450159..55452087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227799	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10176839	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10183953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191785	1.00[CEU][hapmap]
rs10439479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892007	0.82[JPT][hapmap]
rs11904107	0.82[JPT][hapmap]
rs12104902	0.82[JPT][hapmap]
rs12105731	0.82[JPT][hapmap]
rs12464094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12470507	1.00[YRI][hapmap]
rs12617316	0.82[JPT][hapmap]
rs12713290	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002841	0.82[JPT][hapmap]
rs13031346	0.82[JPT][hapmap]
rs1437387	0.82[JPT][hapmap]
rs1437388	0.82[JPT][hapmap]
rs1437389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561231	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561232	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561233	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046834	0.82[JPT][hapmap]
rs17046915	1.00[CEU][hapmap]
rs2028138	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249856	0.82[JPT][hapmap]
rs2289168	0.82[JPT][hapmap]
rs2576692	0.82[JPT][hapmap]
rs2576693	0.82[JPT][hapmap]
rs2576699	0.82[JPT][hapmap]
rs2576702	0.82[JPT][hapmap]
rs2576723	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589060	0.82[JPT][hapmap]
rs2589061	0.82[JPT][hapmap]
rs2589063	0.82[JPT][hapmap]
rs2589081	0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589082	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589083	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2589111	0.82[JPT][hapmap]
rs2589113	0.82[JPT][hapmap]
rs2920845	0.86[EUR][1000 genomes]
rs2920846	0.83[EUR][1000 genomes]
rs2920869	0.86[EUR][1000 genomes]
rs2966465	0.82[JPT][hapmap]
rs2968816	0.82[JPT][hapmap]
rs2968820	0.82[JPT][hapmap]
rs2972087	0.82[JPT][hapmap]
rs4233959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545482	1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs6545484	0.82[JPT][hapmap]
rs6713058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718747	0.82[JPT][hapmap]
rs6719579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726732	0.82[JPT][hapmap]
rs6733567	0.82[JPT][hapmap]
rs6746287	0.82[JPT][hapmap]
rs6746757	1.00[CEU][hapmap]
rs6746983	1.00[CEU][hapmap]
rs6747682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747974	1.00[CEU][hapmap]
rs6750501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754605	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6759310	1.00[CEU][hapmap]
rs6759957	1.00[CEU][hapmap]
rs9784090	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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55424600-55451200	Weak transcription	HepG2	liver
2	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55432000-55451200	Weak transcription	Dnd41	blood
5	chr2:55449400-55451200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:55449600-55451000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:55450000-55450800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr2:55450000-55450800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:55450000-55451000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:55450000-55451000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr2:55450000-55451000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:55450000-55451200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:55450000-55451200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:55450000-55451200	Active TSS	Fetal Kidney	kidney
15	chr2:55450000-55451400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr2:55450000-55451400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:55450000-55451400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr2:55450000-55451400	Active TSS	Duodenum Mucosa	Duodenum
19	chr2:55450000-55451400	Active TSS	A549	lung
20	chr2:55450000-55451600	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr2:55450200-55450600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:55450200-55450600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr2:55450200-55450600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:55450200-55450600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:55450200-55450600	Active TSS	Fetal Brain Male	brain
26	chr2:55450200-55450600	Flanking Active TSS	Fetal Thymus	thymus
27	chr2:55450200-55450600	Active TSS	Right Ventricle	heart
28	chr2:55450200-55450800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr2:55450200-55451000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr2:55450200-55451000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr2:55450200-55451000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:55450200-55451000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:55450200-55451000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:55450200-55451000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:55450200-55451000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55450200-55451000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:55450200-55451000	Active TSS	Aorta	Aorta
38	chr2:55450200-55451000	Active TSS	Brain Angular Gyrus	brain
39	chr2:55450200-55451000	Active TSS	Fetal Brain Female	brain
40	chr2:55450200-55451000	Active TSS	Fetal Intestine Large	intestine
41	chr2:55450200-55451000	Active TSS	Fetal Stomach	stomach
42	chr2:55450200-55451000	Active TSS	Ovary	ovary
43	chr2:55450200-55451000	Active TSS	Placenta Amnion	Placenta Amnion
44	chr2:55450200-55451000	Active TSS	Psoas Muscle	Psoas
45	chr2:55450200-55451000	Active TSS	Right Atrium	heart
46	chr2:55450200-55451000	Active TSS	Stomach Mucosa	stomach
47	chr2:55450200-55451000	Active TSS	GM12878-XiMat	blood
48	chr2:55450200-55451000	Active TSS	HSMM	muscle
49	chr2:55450200-55451000	Active TSS	HSMMtube	muscle
50	chr2:55450200-55451000	Active TSS	NH-A	brain

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