Variant report

Variant	rs1000013
Chromosome Location	chr7:40590569-40590570
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	TCF12	chr7:40590485-40592572	SK-N-SH	brain:	n/a	chr7:40590990-40590999 chr7:40591055-40591064 chr7:40592089-40592099
2	EP300	chr7:40588857-40596953	SK-N-SH	brain:	n/a	chr7:40591110-40591124 chr7:40591855-40591864 chr7:40594897-40594911 chr7:40590048-40590062

Variant related genes	Relation type
ENSG00000203446	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1019018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254954	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10263677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10429076	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10486810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10486811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11973006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11974322	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11977013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs11980464	0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11982075	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171727	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171730	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17171734	0.92[EUR][1000 genomes]
rs17171747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1859660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859705	0.81[ASN][1000 genomes]
rs2329818	0.87[EUR][1000 genomes]
rs2329819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28657711	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34523428	0.89[EUR][1000 genomes]
rs3919491	0.90[EUR][1000 genomes]
rs4720367	0.91[AFR][1000 genomes]
rs4720368	0.89[EUR][1000 genomes]
rs4720370	0.87[EUR][1000 genomes]
rs4720371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723966	0.89[EUR][1000 genomes]
rs4723967	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4723968	0.89[EUR][1000 genomes]
rs4723969	0.89[EUR][1000 genomes]
rs4723970	0.92[EUR][1000 genomes]
rs4723972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57268522	0.87[EUR][1000 genomes]
rs60011074	0.92[EUR][1000 genomes]
rs60999211	0.90[EUR][1000 genomes]
rs61107746	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6462985	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67340458	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6943787	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945570	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6948724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6948900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6954401	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6956277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6977104	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73122188	0.97[ASN][1000 genomes]
rs73308254	0.89[EUR][1000 genomes]
rs73308257	0.89[EUR][1000 genomes]
rs73308260	0.92[EUR][1000 genomes]
rs73308263	0.92[EUR][1000 genomes]
rs73308264	0.95[EUR][1000 genomes]
rs73308269	0.94[EUR][1000 genomes]
rs73308281	0.91[EUR][1000 genomes]
rs73308284	0.92[EUR][1000 genomes]
rs73308289	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73308291	0.90[EUR][1000 genomes]
rs73308300	0.90[EUR][1000 genomes]
rs73310208	0.87[EUR][1000 genomes]
rs7459324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7776976	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs7808612	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917204	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9632613	0.97[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	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1030515	chr7:40501867-40634808	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv830971	chr7:40523075-40700172	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40585000-40591000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:40585000-40591800	Weak transcription	Fetal Stomach	stomach
3	chr7:40585200-40591400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:40585600-40591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:40585600-40591200	Weak transcription	Fetal Kidney	kidney
6	chr7:40585800-40591000	Weak transcription	Fetal Lung	lung
7	chr7:40586600-40591800	Weak transcription	Placenta	Placenta
8	chr7:40586800-40591400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:40586800-40591400	Weak transcription	Aorta	Aorta
10	chr7:40587000-40590600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:40587000-40591000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:40587000-40591000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:40587000-40591000	Weak transcription	NHDF-Ad	bronchial
14	chr7:40587000-40591000	Weak transcription	Osteobl	bone
15	chr7:40587000-40591200	Weak transcription	HMEC	breast
16	chr7:40589000-40591200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr7:40589400-40591200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:40589400-40591600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr7:40589600-40591400	Weak transcription	Left Ventricle	heart
20	chr7:40589800-40591000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:40589800-40591200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:40590000-40595200	Enhancers	Primary hematopoietic stem cells	blood
23	chr7:40590200-40591600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:40590200-40591600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:40590400-40592200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr7:40590400-40592600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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