Variant report

Variant	rs6668948
Chromosome Location	chr1:85757406-85757407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85740717..85742523-chr1:85757083..85759331,2	K562	blood:
2	chr1:85719208..85720970-chr1:85755325..85757545,2	K562	blood:

Variant related genes	Relation type
ENSG00000223653	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747317	0.90[CHB][hapmap]
rs10782542	0.80[CHB][hapmap]
rs10782543	0.90[CHB][hapmap]
rs11161573	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11161585	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576939	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11580090	0.86[ASN][1000 genomes]
rs11583827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585614	0.88[ASN][1000 genomes]
rs11587512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590047	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061305	0.87[ASN][1000 genomes]
rs12061512	0.85[ASN][1000 genomes]
rs12093484	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12405767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12754032	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125445	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2012099	0.84[ASN][1000 genomes]
rs34743622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4949928	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs57483398	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60325409	0.83[ASN][1000 genomes]
rs61771982	0.89[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7554249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9432848	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
3	chr1:85748600-85764000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:85750000-85761400	Weak transcription	Lung	lung
5	chr1:85750000-85762800	Weak transcription	Pancreas	Pancrea
6	chr1:85750400-85762800	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85750800-85763800	Weak transcription	Primary B cells from cord blood	blood
8	chr1:85752200-85762800	Weak transcription	Aorta	Aorta
9	chr1:85752400-85760600	Weak transcription	Fetal Stomach	stomach
10	chr1:85753600-85758400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:85753600-85758600	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:85754200-85758400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:85754400-85757600	Enhancers	NHDF-Ad	bronchial
14	chr1:85754400-85757800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:85755000-85757600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:85755000-85757600	Enhancers	Osteobl	bone
17	chr1:85755000-85757800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr1:85755000-85757800	Enhancers	NH-A	brain
19	chr1:85755000-85758400	Enhancers	NHLF	lung
20	chr1:85755200-85757800	Enhancers	HSMM	muscle
21	chr1:85755400-85757800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:85755800-85758400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:85755800-85763200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:85756000-85758600	Enhancers	HMEC	breast
25	chr1:85756000-85759800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:85756000-85762800	Enhancers	NHEK	skin
27	chr1:85756200-85759800	Weak transcription	HUVEC	blood vessel
28	chr1:85756400-85762600	Weak transcription	Stomach Mucosa	stomach
29	chr1:85756600-85759200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:85756600-85759200	Weak transcription	Esophagus	oesophagus
31	chr1:85756600-85763200	Weak transcription	GM12878-XiMat	blood
32	chr1:85757000-85762800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:85757400-85760600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links