Variant report

Variant	rs4399712
Chromosome Location	chr2:64023807-64023808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64015319..64017822-chr2:64021923..64023829,2	MCF-7	breast:
2	chr2:64023510..64026519-chr2:64063449..64067726,4	K562	blood:

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

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

rs_ID	r²[population]
rs10187013	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs10201844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207847	0.80[AMR][1000 genomes]
rs10211360	0.90[CHB][hapmap]
rs10865343	0.90[CHB][hapmap]
rs11125985	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125986	0.81[EUR][1000 genomes]
rs12612549	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12612596	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613707	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713497	0.89[CHB][hapmap]
rs13006124	0.85[CHB][hapmap]
rs13384707	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1362797	0.82[EUR][1000 genomes]
rs17619717	0.85[CHB][hapmap]
rs2054119	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36042418	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072113	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4359637	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671526	0.88[EUR][1000 genomes]
rs4671528	0.89[CHB][hapmap]
rs4671532	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6546025	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6546026	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs6546027	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6546038	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap]
rs6546039	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6546043	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs6705192	0.80[EUR][1000 genomes]
rs6726257	0.84[CHB][hapmap]
rs6737855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741298	0.89[CHB][hapmap]
rs6741584	0.90[CHB][hapmap]
rs6747307	0.90[CHB][hapmap]
rs7596262	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs7597935	0.84[CHB][hapmap]
rs9309356	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998043	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][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	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63976400-64028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:64018600-64025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:64019000-64029000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:64020400-64032000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:64020800-64025200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:64022800-64024600	Strong transcription	Adipose Nuclei	Adipose
7	chr2:64023000-64024000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:64023400-64024000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:64023400-64024000	Enhancers	Osteobl	bone
10	chr2:64023400-64024200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:64023600-64024200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:64023600-64024200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:64023600-64024600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:64023600-64024600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:64023600-64032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:64023800-64024000	ZNF genes & repeats	Liver	Liver
17	chr2:64023800-64024000	Enhancers	Psoas Muscle	Psoas
18	chr2:64023800-64024400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:64023800-64024400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links