Variant report

Variant	rs11982075
Chromosome Location	chr7:40586674-40586675
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	GATA3	chr7:40586537-40586887	SH-SY5Y	brain:	n/a	n/a
2	USF2	chr7:40586581-40586847	Hela-S3	cervix:	n/a	chr7:40586692-40586703
3	EP300	chr7:40586276-40586867	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chr7:40586319-40586851	SK-N-SH	brain:	n/a	n/a
5	STAT3	chr7:40586591-40586800	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA2	chr7:40586312-40586888	SH-SY5Y	brain:	n/a	n/a
7	USF1	chr7:40586498-40587071	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr7:40586431-40586908	U87	brain:	n/a	n/a
9	USF1	chr7:40586585-40586819	SK-N-SH_RA	brain:	n/a	n/a
10	JUND	chr7:40586551-40586830	K562	blood:	n/a	n/a
11	USF1	chr7:40586533-40586855	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000203446	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1000013	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]
rs1019018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10254954	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10263677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10429076	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10486810	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10486811	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11973006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11974322	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11977013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs11980464	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171730	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17171734	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];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];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859705	0.81[ASN][1000 genomes]
rs2329818	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2329819	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28657711	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34523428	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs3919491	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4720367	0.89[AFR][1000 genomes]
rs4720368	0.89[EUR][1000 genomes]
rs4720370	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs4720371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723966	0.89[EUR][1000 genomes]
rs4723967	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4723968	0.89[EUR][1000 genomes]
rs4723969	0.89[EUR][1000 genomes]
rs4723970	1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs4723972	1.00[CEU][hapmap];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	0.93[ASN][1000 genomes]
rs6462985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67340458	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6943787	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945570	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6948724	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6948900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.97[ASN][1000 genomes]
rs6954401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs6956277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6977104	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7776976	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs7808612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917204	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9632613	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11982075	C7orf36	cis	cerebellum	SCAN
rs11982075	POLD2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40580800-40587000	Enhancers	NHDF-Ad	bronchial
2	chr7:40584400-40589800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:40584600-40587000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:40585000-40591000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:40585000-40591800	Weak transcription	Fetal Stomach	stomach
6	chr7:40585200-40591400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:40585400-40588600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr7:40585600-40590400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:40585600-40591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:40585600-40591200	Weak transcription	Fetal Kidney	kidney
11	chr7:40585800-40591000	Weak transcription	Fetal Lung	lung
12	chr7:40586200-40587000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:40586200-40587000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:40586200-40587000	Enhancers	Osteobl	bone
15	chr7:40586400-40586800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:40586400-40586800	Enhancers	Aorta	Aorta
17	chr7:40586400-40587000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr7:40586400-40587000	Enhancers	HMEC	breast
19	chr7:40586600-40586800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:40586600-40591800	Weak transcription	Placenta	Placenta

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