Variant report

Variant	rs7530502
Chromosome Location	chr1:186435101-186435102
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	TCF12	chr1:186434937-186435499	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:186434952-186435632	SK-N-SH	brain:	n/a	n/a
3	EP300	chr1:186435001-186435667	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr1:186435040-186435451	SK-N-SH	brain:	n/a	chr1:186435169-186435178
5	GATA3	chr1:186434804-186435642	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr1:186435052-186435496	SK-N-SH	brain:	n/a	n/a
7	JUND	chr1:186434979-186435520	SK-N-SH	brain:	n/a	chr1:186435096-186435108
8	JUND	chr1:186434984-186435476	SK-N-SH	brain:	n/a	chr1:186435096-186435108
9	TEAD4	chr1:186434982-186435532	SK-N-SH	brain:	n/a	chr1:186435169-186435178
10	FOSL2	chr1:186435065-186435535	SK-N-SH	brain:	n/a	chr1:186435096-186435108
11	TCF12	chr1:186434947-186435679	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr1:186435029-186435657	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186431573..186434062-chr1:186434612..186436808,2	MCF-7	breast:

Variant related genes	Relation type
PDC	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10158395	0.85[YRI][hapmap]
rs10489394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10489395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494585	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs10494588	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12239085	0.87[AMR][1000 genomes]
rs12239322	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12239327	0.87[AMR][1000 genomes]
rs13374147	0.87[AMR][1000 genomes]
rs13374242	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13375943	0.85[YRI][hapmap]
rs13376114	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13376658	0.87[AMR][1000 genomes]
rs16825179	0.86[YRI][hapmap]
rs16825187	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825277	0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825282	0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825292	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825329	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825448	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825457	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1929094	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3934201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41393449	0.99[AFR][1000 genomes]
rs56158125	0.87[AMR][1000 genomes]
rs56888492	1.00[AMR][1000 genomes]
rs57020506	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57488115	0.87[AMR][1000 genomes]
rs58300321	0.87[AMR][1000 genomes]
rs58336827	0.87[AMR][1000 genomes]
rs58410196	0.87[AMR][1000 genomes]
rs59886878	0.87[AFR][1000 genomes]
rs60957652	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425029	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6673816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679283	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6688055	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695920	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7355201	0.87[AMR][1000 genomes]
rs7355203	1.00[AMR][1000 genomes]
rs7547924	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9803910	0.87[AMR][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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv1824284	chr1:186358588-186441585	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186406600-186450000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:186434400-186435200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:186434400-186435600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:186434400-186435600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:186434400-186435600	Enhancers	Osteobl	bone
6	chr1:186435000-186435400	Enhancers	GM12878-XiMat	blood

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