Variant report

Variant	rs71652602
Chromosome Location	chr1:95509475-95509476
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:95318706..95321767-chr1:95507313..95510717,3	K562	blood:
2	chr1:95285703..95286399-chr1:95508712..95509642,4	MCF-7	breast:
3	chr1:95508625..95509695-chr1:95699228..95700102,5	K562	blood:
4	chr1:95319207..95320829-chr1:95507414..95509861,2	MCF-7	breast:
5	chr1:95285374..95286173-chr1:95508980..95509632,2	MCF-7	breast:
6	chr1:95271098..95272014-chr1:95508742..95509603,4	MCF-7	breast:
7	chr1:95319172..95320847-chr1:95508664..95509618,15	K562	blood:
8	chr1:95271063..95271580-chr1:95508693..95509648,2	K562	blood:
9	chr1:95319681..95320573-chr1:95508384..95509568,5	MCF-7	breast:
10	chr1:95319373..95320645-chr1:95508673..95509610,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224081	Chromatin interaction
ENSG00000143036	Chromatin interaction
ENSG00000226026	Chromatin interaction
ENSG00000122481	Chromatin interaction
ENSG00000237416	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11165297	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590106	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12717800	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12751633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12755096	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12760863	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34726676	0.81[AMR][1000 genomes]
rs35328371	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131811	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6669262	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671842	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6674604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695561	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6698894	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67440829	0.94[EUR][1000 genomes]
rs71652601	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs71654403	0.81[AMR][1000 genomes]
rs74101985	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7540821	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7543156	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9661047	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3402740	chr1:95500980-95527860	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
2	chr1:95489400-95517200	Weak transcription	Aorta	Aorta
3	chr1:95491600-95529600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:95502000-95512200	Weak transcription	GM12878-XiMat	blood
5	chr1:95505600-95537400	Weak transcription	Right Atrium	heart
6	chr1:95505800-95509600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:95506000-95517000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:95506000-95537800	Weak transcription	Pancreas	Pancrea
9	chr1:95506600-95527800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:95508000-95509800	Enhancers	A549	lung
11	chr1:95508000-95513600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:95508200-95510200	Enhancers	NHLF	lung
13	chr1:95508400-95509600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:95508600-95509600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:95508800-95509600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:95508800-95509600	Enhancers	Brain Cingulate Gyrus	brain
17	chr1:95508800-95509800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:95508800-95510000	Enhancers	Liver	Liver
19	chr1:95509000-95509600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:95509000-95509600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:95509000-95509600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:95509000-95510600	Weak transcription	Ovary	ovary
23	chr1:95509000-95510800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:95509000-95514000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:95509000-95528000	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:95509200-95509600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:95509200-95509600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:95509200-95509600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr1:95509200-95525600	Weak transcription	Adipose Nuclei	Adipose
30	chr1:95509400-95509600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:95509400-95515800	Weak transcription	Brain Anterior Caudate	brain
32	chr1:95509400-95527600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:95509400-95532800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:95509400-95534200	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links