Variant report

Variant	rs2060718
Chromosome Location	chr7:128331413-128331414
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	chr7:128331101..128332933-chr7:128334732..128337486,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71F2-4	chr7:128330505-128331771	ENSG00000271344.1

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10954208	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10954209	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10954210	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs11763357	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12532347	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534956	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2003954	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2013189	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3802004	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs56403867	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57185253	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58709686	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58781928	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60117311	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481882	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62481884	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62481903	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62481943	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62483312	0.81[AMR][1000 genomes]
rs6965563	0.84[EUR][1000 genomes]
rs6971091	0.90[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73723614	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs745229	0.95[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap]

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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv966738	chr7:128325654-128339129	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2060718	CICP14	cis	Thyroid	GTEx
rs2060718	RP11-274B21.2	cis	Thyroid	GTEx
rs2060718	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs2060718	RP11-274B21.4	cis	lung	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128302400-128337200	Weak transcription	Gastric	stomach
2	chr7:128313600-128337200	Weak transcription	Right Atrium	heart
3	chr7:128320200-128332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:128320200-128337200	Weak transcription	NHLF	lung
5	chr7:128321000-128332000	Weak transcription	Fetal Brain Male	brain
6	chr7:128322200-128333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:128323400-128337200	Weak transcription	Left Ventricle	heart
8	chr7:128324200-128337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:128324400-128337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:128325600-128333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:128325600-128337000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:128326000-128337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:128328000-128331600	Weak transcription	Aorta	Aorta
14	chr7:128328000-128332800	Weak transcription	Brain Anterior Caudate	brain
15	chr7:128328000-128333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:128328000-128334000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:128328000-128334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:128328000-128337000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:128328000-128337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:128328000-128337200	Weak transcription	HSMMtube	muscle
21	chr7:128328000-128337200	Weak transcription	NH-A	brain
22	chr7:128328200-128337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:128328800-128337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:128329000-128337200	Weak transcription	HSMM	muscle
25	chr7:128329400-128333400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:128329400-128337200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links