Variant report

Variant	rs6778401
Chromosome Location	chr3:160334529-160334530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160331889..160334678-chr3:160367548..160370147,2	K562	blood:
2	chr3:160334213..160336560-chr3:160410896..160413841,2	MCF-7	breast:
3	chr3:160329547..160332346-chr3:160334349..160336341,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10212356	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11919703	0.80[EUR][1000 genomes]
rs13314803	0.80[EUR][1000 genomes]
rs16831286	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16831313	0.94[EUR][1000 genomes]
rs1920661	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs2178454	0.94[EUR][1000 genomes]
rs28631610	0.93[EUR][1000 genomes]
rs55804574	0.94[EUR][1000 genomes]
rs6441326	0.94[EUR][1000 genomes]
rs6778711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813697	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9820919	0.83[AMR][1000 genomes]
rs9825299	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9829578	0.80[EUR][1000 genomes]
rs9838380	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9847211	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9857038	0.94[EUR][1000 genomes]
rs9857327	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160331000-160334600	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:160333600-160336200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:160333800-160335600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160334000-160335000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:160334000-160335000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:160334000-160335000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:160334000-160335000	Enhancers	NH-A	brain
8	chr3:160334000-160335200	Enhancers	NHEK	skin
9	chr3:160334000-160335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:160334000-160335400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:160334000-160335400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:160334000-160335400	Enhancers	HMEC	breast
13	chr3:160334000-160336200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:160334200-160334600	Enhancers	NHLF	lung
15	chr3:160334200-160334800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:160334200-160334800	Enhancers	Left Ventricle	heart
17	chr3:160334200-160335000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:160334200-160335000	Enhancers	HSMM	muscle
19	chr3:160334200-160335600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:160334200-160335600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:160334200-160336400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:160334200-160336400	Enhancers	Pancreas	Pancrea
23	chr3:160334200-160336400	Enhancers	Psoas Muscle	Psoas
24	chr3:160334200-160336400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:160334200-160336400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:160334400-160334800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:160334400-160335000	Enhancers	Stomach Smooth Muscle	stomach
28	chr3:160334400-160335000	Enhancers	Osteobl	bone
29	chr3:160334400-160335800	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links