Variant report

Variant	rs6718747
Chromosome Location	chr2:55508618-55508619
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	JUN	chr2:55508433-55508633	HepG2	liver:	n/a	chr2:55508531-55508540 chr2:55508533-55508540
2	E2F6	chr2:55508497-55509857	H1-hESC	embryonic stem cell:	n/a	chr2:55509235-55509245
3	FOS	chr2:55508441-55508692	MCF10A-Er-Src	breast:	n/a	chr2:55508531-55508540 chr2:55508533-55508540
4	FOS	chr2:55508354-55508688	MCF10A-Er-Src	breast:	n/a	chr2:55508531-55508540 chr2:55508533-55508540
5	CUX1	chr2:55508472-55508798	K562	blood:	n/a	n/a
6	POLR2A	chr2:55508527-55510140	GM12878	blood:	n/a	n/a
7	JUND	chr2:55508358-55508705	HepG2	liver:	n/a	chr2:55508530-55508541 chr2:55508531-55508540 chr2:55508533-55508540
8	JUND	chr2:55508527-55508727	K562	blood:	n/a	chr2:55508530-55508541 chr2:55508531-55508540 chr2:55508533-55508540
9	JUND	chr2:55508513-55508675	H1-hESC	embryonic stem cell:	n/a	chr2:55508530-55508541 chr2:55508531-55508540 chr2:55508533-55508540
10	MAX	chr2:55508562-55510255	A549	lung:	n/a	n/a
11	FOS	chr2:55508370-55508702	MCF10A-Er-Src	breast:	n/a	chr2:55508531-55508540 chr2:55508533-55508540
12	FOS	chr2:55508429-55508653	MCF10A-Er-Src	breast:	n/a	chr2:55508531-55508540 chr2:55508533-55508540

No.	Distal block	Cell Line	Cell type
1	chr2:55508571..55512777-chr2:55645734..55648780,3	K562	blood:
2	chr2:55508376..55510742-chr2:55843787..55846796,4	K562	blood:
3	chr2:55496311..55498089-chr2:55508225..55509799,2	MCF-7	breast:
4	chr2:55507639..55510296-chr2:55843126..55844712,2	K562	blood:
5	chr2:55494928..55498059-chr2:55506695..55512310,8	K562	blood:
6	chr2:55491409..55498987-chr2:55507178..55511380,11	MCF-7	breast:
7	chr2:55507859..55511177-chr2:55645007..55647398,3	K562	blood:
8	chr2:55450683..55452300-chr2:55507599..55509366,2	K562	blood:
9	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206964	TF binding region
PRORSD1P	TF binding region
ENSG00000115355	Chromatin interaction
ENSG00000227799	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10183953	0.82[JPT][hapmap]
rs10209598	1.00[ASN][1000 genomes]
rs10439479	0.82[JPT][hapmap]
rs10496041	0.94[ASN][1000 genomes]
rs11125562	1.00[ASN][1000 genomes]
rs11694920	0.82[JPT][hapmap]
rs11892007	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11904107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12104902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs12105322	1.00[ASN][1000 genomes]
rs12105731	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12617316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016664	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031346	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13407931	1.00[ASN][1000 genomes]
rs1437387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1437388	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1437389	0.82[JPT][hapmap]
rs1437392	0.82[JPT][hapmap]
rs1545120	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545121	0.82[GIH][hapmap]
rs1561231	0.82[JPT][hapmap]
rs17046834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2043714	0.82[JPT][hapmap]
rs2118283	0.82[JPT][hapmap]
rs2249856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289168	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2576691	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576694	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576697	1.00[ASN][1000 genomes]
rs2576698	1.00[ASN][1000 genomes]
rs2576699	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2576702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589081	0.82[JPT][hapmap]
rs2589082	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2589110	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589111	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589112	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589113	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589114	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589115	0.85[ASN][1000 genomes]
rs2589116	1.00[ASN][1000 genomes]
rs2589117	1.00[ASN][1000 genomes]
rs2917781	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920959	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920972	1.00[ASN][1000 genomes]
rs2966465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233959	0.82[JPT][hapmap]
rs4591380	0.82[JPT][hapmap]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545476	0.82[JPT][hapmap]
rs6545479	0.82[JPT][hapmap]
rs6545482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705991	1.00[ASN][1000 genomes]
rs6713058	0.82[JPT][hapmap]
rs6715694	0.82[JPT][hapmap]
rs6716066	0.82[JPT][hapmap]
rs6719579	0.82[JPT][hapmap]
rs6721211	1.00[ASN][1000 genomes]
rs6723870	0.82[JPT][hapmap]
rs6726732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6733567	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs6740631	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6747682	0.82[JPT][hapmap]
rs6750501	0.82[JPT][hapmap]
rs73939905	1.00[ASN][1000 genomes]
rs9784090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55496600-55508800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:55497000-55508800	Weak transcription	Right Atrium	heart
3	chr2:55497400-55508800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:55497600-55508800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
6	chr2:55504800-55508800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55505400-55508800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55505400-55508800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:55505600-55508800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:55506600-55508800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:55506800-55508800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:55506800-55508800	Weak transcription	Pancreas	Pancrea
13	chr2:55507000-55508800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:55507400-55508800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:55507400-55509000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55507400-55509000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:55507600-55508800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:55507600-55509000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:55507600-55509400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:55507800-55508800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:55507800-55508800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:55507800-55508800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr2:55507800-55508800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:55507800-55508800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:55507800-55508800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:55507800-55508800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:55507800-55508800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:55507800-55508800	Weak transcription	HSMMtube	muscle
29	chr2:55507800-55509000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55507800-55509000	Enhancers	HMEC	breast
31	chr2:55507800-55509200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:55507800-55509200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:55507800-55509400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:55508000-55508800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:55508000-55508800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:55508000-55510600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:55508400-55508800	Enhancers	Colonic Mucosa	Colon
38	chr2:55508400-55509400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:55508600-55508800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr2:55508600-55508800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:55508600-55508800	Enhancers	Primary B cells from cord blood	blood
42	chr2:55508600-55508800	Enhancers	Primary B cells from peripheral blood	blood
43	chr2:55508600-55508800	Enhancers	Primary hematopoietic stem cells	blood
44	chr2:55508600-55508800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr2:55508600-55508800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55508600-55508800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:55508600-55508800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:55508600-55508800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:55508600-55508800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:55508600-55508800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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