Variant report

Variant	rs4656288
Chromosome Location	chr1:161066446-161066447
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	ZNF143	chr1:161065818-161066451	GM12878	blood:	n/a	chr1:161066417-161066435
2	RELA	chr1:161065703-161066543	GM18951	blood:	n/a	n/a
3	IKZF1	chr1:161065749-161066609	GM12878	blood:	n/a	n/a
4	E2F4	chr1:161066443-161066720	MCF10A-Er-Src	breast:	n/a	n/a
5	EBF1	chr1:161066433-161066809	GM12878	blood:	n/a	n/a
6	ZZZ3	chr1:161065868-161066552	GM12878	blood:	n/a	n/a
7	FOS	chr1:161066393-161066718	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr1:161066444-161066631	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr1:161066409-161066670	A549	lung:	n/a	chr1:161066563-161066580 chr1:161066566-161066579
10	CEBPB	chr1:161066425-161066707	K562	blood:	n/a	chr1:161066563-161066580 chr1:161066566-161066579
11	WRNIP1	chr1:161065798-161066661	GM12878	blood:	n/a	n/a
12	STAT5A	chr1:161065664-161066553	GM12878	blood:	n/a	n/a
13	RELA	chr1:161065763-161066473	GM10847	blood:	n/a	n/a
14	CEBPB	chr1:161066387-161066742	Hela-S3	cervix:	n/a	chr1:161066563-161066580 chr1:161066566-161066579
15	ESRRA	chr1:161065441-161066960	GM12878	blood:	n/a	chr1:161066660-161066676 chr1:161066038-161066048 chr1:161066038-161066048 chr1:161066670-161066686 chr1:161066036-161066049 chr1:161066036-161066052 chr1:161066660-161066676
16	FOS	chr1:161066404-161066775	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPB	chr1:161066412-161066737	IMR90	lung:	n/a	chr1:161066563-161066580 chr1:161066566-161066579
18	MYC	chr1:161066438-161066690	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr1:161066355-161066736	MCF10A-Er-Src	breast:	n/a	n/a
20	CEBPB	chr1:161066399-161066718	MCF-7	breast:	n/a	chr1:161066563-161066580 chr1:161066566-161066579
21	SPI1	chr1:161065729-161066491	GM12891	blood:	n/a	chr1:161065986-161065995 chr1:161066388-161066395
22	FOS	chr1:161066429-161066745	MCF10A-Er-Src	breast:	n/a	n/a
23	SPI1	chr1:161065690-161066550	GM12891	blood:	n/a	chr1:161065986-161065995 chr1:161066388-161066395
24	MTA3	chr1:161065622-161066541	GM12878	blood:	n/a	n/a
25	SPI1	chr1:161065767-161066497	GM12878	blood:	n/a	chr1:161065986-161065995 chr1:161066388-161066395
26	NFIC	chr1:161065596-161066529	GM12878	blood:	n/a	n/a
27	RELA	chr1:161065801-161066591	GM19099	blood:	n/a	n/a
28	STAT3	chr1:161066384-161066668	MCF10A-Er-Src	breast:	n/a	n/a
29	SPI1	chr1:161065606-161066612	GM12878	blood:	n/a	chr1:161065986-161065995 chr1:161066388-161066395

No.	Distal block	Cell Line	Cell type
1	chr1:161013722..161017299-chr1:161066199..161071039,5	MCF-7	breast:
2	chr1:161064725..161068388-chr1:161069127..161071844,3	MCF-7	breast:
3	chr1:160987801..160992609-chr1:161065993..161069595,4	MCF-7	breast:
4	chr1:160972087..160975048-chr1:161066232..161067921,2	MCF-7	breast:
5	chr1:161014309..161017739-chr1:161064390..161068099,3	K562	blood:
6	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
7	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:
8	chr1:161006620..161008413-chr1:161065670..161068063,2	MCF-7	breast:

Variant related genes	Relation type
KLHDC9	TF binding region
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000270149	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11265549	0.80[CEU][hapmap]
rs12401309	0.84[GIH][hapmap];0.83[TSI][hapmap]
rs1467742	0.88[GIH][hapmap]
rs3820097	0.88[GIH][hapmap];0.82[MEX][hapmap]
rs3892376	0.82[MEX][hapmap]
rs4233364	0.90[CEU][hapmap]
rs4656287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656979	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656981	0.91[ASN][1000 genomes]
rs72480265	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
2	chr1:161061200-161067000	Weak transcription	Primary T cells from cord blood	blood
3	chr1:161061400-161066800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:161062600-161067800	Weak transcription	Lung	lung
5	chr1:161062800-161066800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:161062800-161067600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:161063000-161067200	Weak transcription	A549	lung
8	chr1:161063200-161066800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:161063200-161067000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:161063200-161067200	Weak transcription	NH-A	brain
11	chr1:161063400-161066600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:161063400-161067200	Weak transcription	Osteobl	bone
13	chr1:161065000-161066600	Weak transcription	Fetal Lung	lung
14	chr1:161065200-161067000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:161065200-161067000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:161065400-161067600	Enhancers	Placenta	Placenta
17	chr1:161065600-161067600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:161065600-161067600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:161065800-161067000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:161065800-161067600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:161065800-161067600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:161065800-161067600	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:161065800-161067600	Enhancers	Fetal Muscle Leg	muscle
24	chr1:161065800-161067600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:161066000-161067200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:161066000-161067200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:161066000-161067200	Enhancers	NHDF-Ad	bronchial
28	chr1:161066000-161067600	Enhancers	Primary B cells from cord blood	blood
29	chr1:161066000-161067600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:161066000-161067600	Enhancers	Adipose Nuclei	Adipose
31	chr1:161066000-161067600	Enhancers	HMEC	breast
32	chr1:161066000-161067600	Enhancers	NHEK	skin
33	chr1:161066000-161067800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:161066000-161067800	Enhancers	HSMM	muscle
35	chr1:161066200-161067200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:161066200-161067400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:161066200-161067400	Enhancers	HSMMtube	muscle
38	chr1:161066200-161067600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:161066200-161067600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:161066200-161067600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr1:161066200-161067600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:161066200-161067600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:161066200-161067600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:161066200-161067600	Enhancers	Fetal Stomach	stomach
45	chr1:161066200-161067600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:161066400-161066800	Weak transcription	Esophagus	oesophagus
47	chr1:161066400-161066800	Enhancers	GM12878-XiMat	blood
48	chr1:161066400-161067000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:161066400-161067200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:161066400-161067200	Weak transcription	Spleen	Spleen

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