Variant report

Variant	rs6428400
Chromosome Location	chr1:197392460-197392461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10801603	0.83[YRI][hapmap]
rs11799366	1.00[AMR][1000 genomes]
rs11800199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11802844	1.00[AMR][1000 genomes]
rs11802964	1.00[AMR][1000 genomes]
rs11803371	1.00[AMR][1000 genomes]
rs11804057	1.00[AMR][1000 genomes]
rs11805327	1.00[AMR][1000 genomes]
rs11805755	1.00[AMR][1000 genomes]
rs11805909	1.00[AMR][1000 genomes]
rs11806221	1.00[AMR][1000 genomes]
rs11806278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806385	1.00[AMR][1000 genomes]
rs11807556	1.00[AMR][1000 genomes]
rs11807717	1.00[AMR][1000 genomes]
rs11808659	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11809220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11809987	1.00[AMR][1000 genomes]
rs16841475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16841850	1.00[AMR][1000 genomes]
rs2476023	0.82[YRI][hapmap]
rs34240488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3888103	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6428399	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657488	1.00[AMR][1000 genomes]
rs6666890	1.00[AMR][1000 genomes]
rs6667162	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs6667565	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6697556	1.00[AMR][1000 genomes]
rs6703514	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6703515	1.00[AMR][1000 genomes]
rs7522037	1.00[AMR][1000 genomes]
rs7533154	1.00[AMR][1000 genomes]
rs7535981	1.00[AMR][1000 genomes]
rs7543290	1.00[AMR][1000 genomes]
rs7554788	1.00[AMR][1000 genomes]
rs9661515	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197388800-197407000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197388800-197407000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:197389400-197393400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:197389600-197405800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:197391200-197393400	Weak transcription	Fetal Brain Female	brain
6	chr1:197391600-197393000	Enhancers	Hela-S3	cervix
7	chr1:197391600-197398400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:197391800-197392600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:197392000-197392800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:197392000-197393000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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