Variant report

Variant	rs1228860
Chromosome Location	chr7:84001985-84001986
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	NFIC	chr7:84001143-84002098	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr7:84001298-84002008	U87	brain:	n/a	n/a
3	FOSL2	chr7:84001330-84002153	SK-N-SH	brain:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
4	EGR1	chr7:84001586-84002174	HCT-116	colon:	n/a	chr7:84001829-84001840 chr7:84001827-84001842
5	PBX3	chr7:84001306-84002089	SK-N-SH	brain:	n/a	n/a
6	EGR1	chr7:84001606-84002013	ECC-1	luminal epithelium:	n/a	chr7:84001829-84001840 chr7:84001827-84001842
7	POLR2A	chr7:84001139-84002162	U87	brain:	n/a	n/a
8	MAFK	chr7:84001367-84002335	IMR90	lung:	n/a	n/a
9	EP300	chr7:84001246-84002019	SK-N-SH_RA	brain:	n/a	chr7:84001860-84001869
10	PBX3	chr7:84001257-84002052	SK-N-SH	brain:	n/a	n/a
11	EP300	chr7:84001240-84002080	SK-N-SH	brain:	n/a	chr7:84001860-84001869
12	JUND	chr7:84001082-84002582	SK-N-SH	brain:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001859-84001870 chr7:84001860-84001870 chr7:84001860-84001870
13	TCF12	chr7:84001270-84002097	SK-N-SH	brain:	n/a	n/a
14	FOSL2	chr7:84001356-84002089	SK-N-SH	brain:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
15	FOS	chr7:84001460-84002048	MCF10A-Er-Src	breast:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
16	STAT3	chr7:84001029-84002054	MCF10A-Er-Src	breast:	n/a	chr7:84001861-84001870
17	FOS	chr7:84001408-84002066	MCF10A-Er-Src	breast:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
18	GATA3	chr7:84001129-84002107	SK-N-SH	brain:	n/a	chr7:84001862-84001871
19	TAF1	chr7:84001420-84002007	PFSK-1	brain:	n/a	n/a
20	JUND	chr7:84001316-84002184	SK-N-SH	brain:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001859-84001870 chr7:84001860-84001870 chr7:84001860-84001870
21	JUND	chr7:84001300-84002143	SK-N-SH	brain:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001859-84001870 chr7:84001860-84001870 chr7:84001860-84001870
22	FOS	chr7:84001449-84002009	MCF10A-Er-Src	breast:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
23	NFIC	chr7:84001384-84002037	SK-N-SH	brain:	n/a	n/a
24	GATA3	chr7:84001196-84002047	SK-N-SH	brain:	n/a	chr7:84001862-84001871
25	FOS	chr7:84001555-84002046	MCF10A-Er-Src	breast:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
26	RXRA	chr7:84001329-84002084	SK-N-SH	brain:	n/a	chr7:84001860-84001869
27	FOSL1	chr7:84001652-84002108	HCT-116	colon:	n/a	chr7:84001860-84001870 chr7:84001860-84001870 chr7:84001861-84001870 chr7:84001860-84001870 chr7:84001860-84001870
28	CEBPB	chr7:84001466-84002449	IMR90	lung:	n/a	chr7:84002235-84002246
29	TCF12	chr7:84001235-84002158	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr7:84001382-84001992	SK-N-SH_RA	brain:	n/a	n/a
31	SPI1	chr7:84001903-84002493	HL-60	blood:	n/a	n/a
32	POLR2A	chr7:84001221-84002185	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
SEMA3A	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10236082	0.81[EUR][1000 genomes]
rs10255354	0.85[EUR][1000 genomes]
rs10954752	0.81[EUR][1000 genomes]
rs10954753	0.81[EUR][1000 genomes]
rs11972641	0.81[EUR][1000 genomes]
rs11973476	0.84[EUR][1000 genomes]
rs1228859	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228866	0.84[EUR][1000 genomes]
rs1228867	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228868	0.82[EUR][1000 genomes]
rs1228875	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228876	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228878	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228879	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1228880	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1228882	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228883	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1228939	0.90[CEU][hapmap]
rs1228952	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228953	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228954	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228958	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228959	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228961	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1228963	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1234535	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12707647	0.81[EUR][1000 genomes]
rs13227369	0.86[EUR][1000 genomes]
rs13238916	0.84[EUR][1000 genomes]
rs13437801	0.81[EUR][1000 genomes]
rs1557791	0.88[EUR][1000 genomes]
rs1634614	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1715510	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1733998	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1733999	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1974512	0.84[EUR][1000 genomes]
rs1987325	0.84[EUR][1000 genomes]
rs2106965	0.88[EUR][1000 genomes]
rs2158169	0.85[EUR][1000 genomes]
rs2189119	0.81[EUR][1000 genomes]
rs2214362	0.84[EUR][1000 genomes]
rs2372453	0.85[EUR][1000 genomes]
rs2428808	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2522371	0.83[EUR][1000 genomes]
rs2681435	0.82[EUR][1000 genomes]
rs2888321	0.85[EUR][1000 genomes]
rs4728554	0.84[EUR][1000 genomes]
rs4732548	0.81[EUR][1000 genomes]
rs4732549	0.84[EUR][1000 genomes]
rs505758	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs519663	0.84[EUR][1000 genomes]
rs521595	0.83[EUR][1000 genomes]
rs524163	0.80[EUR][1000 genomes]
rs524301	0.83[EUR][1000 genomes]
rs530698	0.84[EUR][1000 genomes]
rs538712	0.82[EUR][1000 genomes]
rs539643	0.84[EUR][1000 genomes]
rs540454	0.84[EUR][1000 genomes]
rs549975	0.84[EUR][1000 genomes]
rs560627	0.81[EUR][1000 genomes]
rs561955	0.83[EUR][1000 genomes]
rs568973	0.84[EUR][1000 genomes]
rs577142	0.86[EUR][1000 genomes]
rs607120	0.84[EUR][1000 genomes]
rs608459	0.84[EUR][1000 genomes]
rs609308	0.84[EUR][1000 genomes]
rs611442	0.84[EUR][1000 genomes]
rs611503	0.84[EUR][1000 genomes]
rs612337	0.81[EUR][1000 genomes]
rs612856	0.84[EUR][1000 genomes]
rs613335	0.84[EUR][1000 genomes]
rs620892	0.85[EUR][1000 genomes]
rs621903	0.84[EUR][1000 genomes]
rs623289	0.83[EUR][1000 genomes]
rs62474863	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs625480	0.84[EUR][1000 genomes]
rs633234	0.82[EUR][1000 genomes]
rs642572	0.81[EUR][1000 genomes]
rs648653	0.81[EUR][1000 genomes]
rs7789787	0.84[EUR][1000 genomes]
rs7808081	0.84[EUR][1000 genomes]
rs916865	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs961201	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv2754468	chr7:83851249-84166749	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv888631	chr7:83911271-84010005	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1023848	chr7:83985028-84101774	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2761342	chr7:83985028-84101798	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv534431	chr7:84001059-84138511	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:84001000-84002600	Enhancers	NHLF	lung
2	chr7:84001000-84002600	Enhancers	Osteobl	bone
3	chr7:84001200-84002600	Enhancers	HSMM	muscle
4	chr7:84001200-84002800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:84001200-84002800	Enhancers	NHDF-Ad	bronchial
6	chr7:84001400-84002000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:84001400-84002000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:84001400-84002200	Enhancers	HMEC	breast
9	chr7:84001400-84002600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:84001400-84003800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:84001600-84002000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:84001600-84002200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:84001600-84002600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:84001600-84002600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:84001600-84002600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr7:84001600-84002600	Enhancers	NH-A	brain
17	chr7:84001600-84003400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:84001800-84002200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:84001800-84002600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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