Variant report

Variant	rs16864479
Chromosome Location	chr2:177679492-177679493
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	RAD21	chr2:177679460-177679842	Hela-S3	cervix:	n/a	chr2:177679679-177679698
2	SIN3AK20	chr2:177678831-177679678	MCF-7	breast:	n/a	n/a
3	GATA2	chr2:177679436-177679741	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr2:177679482-177679788	K562	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
5	GATA3	chr2:177679308-177679841	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr2:177679465-177679878	MCF-7	breast:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
7	CTCF	chr2:177679460-177679610	HCT-116	colon:	n/a	n/a
8	RAD21	chr2:177679462-177679882	H1-hESC	embryonic stem cell:	n/a	chr2:177679679-177679698
9	RAD21	chr2:177679481-177679825	K562	blood:	n/a	chr2:177679679-177679698
10	RAD21	chr2:177679388-177679850	ECC-1	luminal epithelium:	n/a	chr2:177679679-177679698
11	RAD21	chr2:177679395-177679853	SK-N-SH_RA	brain:	n/a	chr2:177679679-177679698
12	ZNF143	chr2:177679491-177679857	GM12878	blood:	n/a	n/a
13	RAD21	chr2:177679444-177679846	GM12878	blood:	n/a	chr2:177679679-177679698
14	CTCF	chr2:177679439-177679828	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
15	RAD21	chr2:177679455-177679829	SK-N-SH_RA	brain:	n/a	chr2:177679679-177679698
16	CTCF	chr2:177679162-177680329	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
17	RAD21	chr2:177679489-177679841	GM12878	blood:	n/a	chr2:177679679-177679698
18	RAD21	chr2:177679463-177679743	HepG2	liver:	n/a	chr2:177679679-177679698
19	FOXM1	chr2:177678797-177679678	MCF-7	breast:	n/a	n/a
20	GATA3	chr2:177678685-177680112	MCF-7	breast:	n/a	n/a
21	RAD21	chr2:177679431-177679887	GM12878	blood:	n/a	chr2:177679679-177679698
22	RAD21	chr2:177679425-177679758	H1-hESC	embryonic stem cell:	n/a	chr2:177679679-177679698
23	GATA1	chr2:177679465-177679856	PBDEFetal	blood:	n/a	n/a
24	CTCF	chr2:177679454-177679851	IMR90	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
25	EP300	chr2:177678882-177679720	MCF-7	breast:	n/a	chr2:177679140-177679150 chr2:177679630-177679644
26	CTCF	chr2:177679469-177680017	GM12878	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
27	FOSL2	chr2:177678891-177679569	MCF-7	breast:	n/a	n/a
28	ZNF217	chr2:177679004-177679694	MCF-7	breast:	n/a	n/a
29	RAD21	chr2:177679429-177679887	H1-hESC	embryonic stem cell:	n/a	chr2:177679679-177679698
30	CTCF	chr2:177679460-177679610	A549	lung:	n/a	n/a
31	GATA3	chr2:177678830-177679904	MCF-7	breast:	n/a	n/a
32	SMC3	chr2:177679447-177680006	GM12878	blood:	n/a	n/a
33	RAD21	chr2:177678933-177679909	MCF-7	breast:	n/a	chr2:177679679-177679698
34	ARID3A	chr2:177679462-177679843	K562	blood:	n/a	n/a
35	CTCF	chr2:177679468-177679762	ECC-1	luminal epithelium:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
36	SIN3A	chr2:177679464-177679795	H1-hESC	embryonic stem cell:	n/a	n/a
37	SMC3	chr2:177679453-177680048	Hela-S3	cervix:	n/a	n/a
38	RAD21	chr2:177679438-177679956	A549	lung:	n/a	chr2:177679679-177679698
39	CTCF	chr2:177679440-177679954	MCF-7	breast:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
40	CTCF	chr2:177679480-177679630	HAc	cerebellar:	n/a	n/a
41	CTCF	chr2:177679452-177679992	K562	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
42	EP300	chr2:177678911-177679514	MCF-7	breast:	n/a	chr2:177679140-177679150
43	GATA3	chr2:177679052-177679765	MCF-7	breast:	n/a	n/a
44	GATA3	chr2:177679004-177679715	MCF-7	breast:	n/a	n/a
45	GATA3	chr2:177679357-177679924	A549	lung:	n/a	n/a
46	CTCF	chr2:177679460-177679610	RPTEC	kidney:	n/a	n/a
47	GATA3	chr2:177679335-177679913	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr2:177678869-177679996	MCF-7	breast:	n/a	chr2:177679679-177679698
49	HDAC2	chr2:177678918-177679782	MCF-7	breast:	n/a	chr2:177679140-177679149
50	RAD21	chr2:177679046-177680270	SK-N-SH	brain:	n/a	chr2:177679679-177679698

No.	Distal block	Cell Line	Cell type
1	chr2:177004878..177006132-chr2:177679220..177679989,4	MCF-7	breast:
2	chr2:177516751..177517622-chr2:177679221..177680084,2	MCF-7	breast:
3	chr2:177518427..177519228-chr2:177679235..177679802,3	MCF-7	breast:
4	chr2:177678711..177679684-chr2:177710502..177711032,2	MCF-7	breast:
5	chr2:177543870..177544476-chr2:177679175..177679998,2	MCF-7	breast:
6	chr2:177516771..177517762-chr2:177679104..177680158,5	MCF-7	breast:
7	chr2:177672353..177675128-chr2:177678147..177680944,2	K562	blood:
8	chr2:177610086..177610770-chr2:177679196..177679715,2	MCF-7	breast:
9	chr2:177518336..177518879-chr2:177679032..177679756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223777	TF binding region
ENSG00000223777	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10181816	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12469347	1.00[CHB][hapmap]
rs12693105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1437725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1533303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1545138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864475	0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4021386	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55681572	0.86[ASN][1000 genomes]
rs56234839	0.83[ASN][1000 genomes]
rs6740977	0.95[ASN][1000 genomes]
rs72936904	0.91[ASN][1000 genomes]
rs7588841	1.00[CHB][hapmap]
rs7601162	0.95[ASN][1000 genomes]
rs840698	1.00[CHB][hapmap]
rs840699	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177676800-177679600	Enhancers	Fetal Lung	lung
2	chr2:177677200-177679600	Enhancers	Ovary	ovary
3	chr2:177677400-177681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:177678000-177680200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:177678200-177679600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:177678200-177679600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:177678200-177679600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:177678200-177679600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:177678200-177679600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:177678200-177683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:177678400-177679600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:177678600-177681600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:177678600-177683200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:177678800-177679600	Enhancers	Liver	Liver
15	chr2:177678800-177679600	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:177679000-177683400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:177679200-177679600	Enhancers	HepG2	liver
18	chr2:177679200-177680000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:177679400-177679600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:177679400-177679600	Enhancers	Primary T cells from cord blood	blood
21	chr2:177679400-177679600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:177679400-177679600	Enhancers	Brain Anterior Caudate	brain
23	chr2:177679400-177679600	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:177679400-177679600	Enhancers	Brain Substantia Nigra	brain
25	chr2:177679400-177679600	Enhancers	Fetal Kidney	kidney
26	chr2:177679400-177680000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:177679400-177680200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:177679400-177681000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:177679400-177681200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:177679400-177681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:177679400-177681600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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