Variant report

Variant	rs2141668
Chromosome Location	chr3:160336032-160336033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160334651..160337629-chr3:160364585..160366181,2	MCF-7	breast:
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: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10460866	0.85[ASN][1000 genomes]
rs10936203	0.84[EUR][1000 genomes]
rs10936210	0.81[EUR][1000 genomes]
rs11711627	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712392	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713230	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11721112	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11927913	0.81[EUR][1000 genomes]
rs12152435	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12630956	0.83[EUR][1000 genomes]
rs12638633	0.86[EUR][1000 genomes]
rs12639488	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13062928	0.80[ASN][1000 genomes]
rs13065269	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074231	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075424	0.91[ASN][1000 genomes]
rs13085507	0.80[ASN][1000 genomes]
rs1522285	0.82[EUR][1000 genomes]
rs16831337	0.81[EUR][1000 genomes]
rs17826257	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882125	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1920650	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920663	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1980277	0.82[EUR][1000 genomes]
rs2178451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35008770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498840	0.80[ASN][1000 genomes]
rs4679892	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4679903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679904	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57718211	0.80[ASN][1000 genomes]
rs6803670	0.82[EUR][1000 genomes]
rs71314011	0.85[ASN][1000 genomes]
rs73875285	0.84[EUR][1000 genomes]
rs73875290	0.86[EUR][1000 genomes]
rs7610939	0.81[EUR][1000 genomes]
rs7634255	0.87[ASN][1000 genomes]
rs7644186	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2141668	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160333600-160336200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:160334000-160336200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:160334200-160336400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:160334200-160336400	Enhancers	Pancreas	Pancrea
5	chr3:160334200-160336400	Enhancers	Psoas Muscle	Psoas
6	chr3:160334200-160336400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:160334200-160336400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:160335000-160336200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:160335000-160336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:160335000-160336200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:160335200-160336200	Enhancers	Fetal Intestine Large	intestine
12	chr3:160335200-160336200	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr3:160335400-160336200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:160335400-160336200	Enhancers	Stomach Mucosa	stomach
15	chr3:160335400-160336400	Weak transcription	HMEC	breast
16	chr3:160335600-160336200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:160335600-160337400	Enhancers	Adipose Nuclei	Adipose
18	chr3:160335800-160336200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr3:160335800-160337400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:160336000-160336200	Enhancers	Fetal Intestine Small	intestine
21	chr3:160336000-160336400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:160336000-160336400	Enhancers	Aorta	Aorta
23	chr3:160336000-160336400	Flanking Active TSS	Liver	Liver
24	chr3:160336000-160336600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links