Variant report

Variant	rs12404700
Chromosome Location	chr1:180286657-180286658
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180282396..180285263-chr1:180286610..180289020,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10494526	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913960	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913962	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913963	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913964	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913967	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913975	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913977	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12022629	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12037744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12069143	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089448	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403226	0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12409923	0.80[ASN][1000 genomes]
rs2025593	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2764460	0.87[ASN][1000 genomes]
rs2877481	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36088499	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878641	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer 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 miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180257600-180289600	Weak transcription	Hela-S3	cervix
2	chr1:180257800-180287200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:180257800-180296200	Weak transcription	Left Ventricle	heart
4	chr1:180278000-180298200	Weak transcription	Esophagus	oesophagus
5	chr1:180278800-180296000	Weak transcription	Pancreas	Pancrea
6	chr1:180279000-180297600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:180279200-180288000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:180279400-180288000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:180279400-180295400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:180279600-180298800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:180281000-180286800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:180281000-180295000	Weak transcription	Fetal Stomach	stomach
13	chr1:180281000-180295200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:180281000-180329400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:180282800-180295400	Weak transcription	Primary B cells from cord blood	blood
16	chr1:180282800-180313400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:180283000-180288000	Weak transcription	HSMM	muscle
18	chr1:180283000-180295000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:180283000-180302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:180283000-180302800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:180285600-180287800	Weak transcription	Ovary	ovary
22	chr1:180286600-180286800	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links