Variant report

Variant	rs2932570
Chromosome Location	chr1:151986820-151986821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:151985949-151986908	A549	lung:	n/a	chr1:151986298-151986316
2	CTCF	chr1:151986680-151986830	RPTEC	kidney:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151964978..151966763-chr1:151984621..151987442,2	K562	blood:
2	chr1:151857351..151860092-chr1:151985508..151987866,2	MCF-7	breast:
3	chr1:151880783..151882439-chr1:151984923..151987759,2	MCF-7	breast:
4	chr1:151978814..151981429-chr1:151985476..151987794,2	K562	blood:
5	chr1:151881612..151883127-chr1:151984846..151987615,2	MCF-7	breast:
6	chr1:151973932..151974613-chr1:151985782..151987112,4	MCF-7	breast:
7	chr1:151906193..151906890-chr1:151985331..151986972,5	MCF-7	breast:
8	chr1:151972758..151974972-chr1:151986628..151989448,2	K562	blood:
9	chr1:151986485..151988607-chr1:151992304..151995986,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240667	TF binding region
ENSG00000197747	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038747	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs10788820	0.81[JPT][hapmap]
rs11204922	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12083193	0.86[CHB][hapmap]
rs12116923	0.86[JPT][hapmap]
rs12410789	0.87[ASN][1000 genomes]
rs1532133	1.00[CHB][hapmap]
rs16833728	0.81[CHB][hapmap]
rs16833743	0.82[CHB][hapmap]
rs1979637	0.95[CHB][hapmap]
rs1994606	0.84[ASN][1000 genomes]
rs2279501	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2279502	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2338019	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932574	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932590	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999526	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2999528	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999531	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2999534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999539	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999560	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999561	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007670	0.80[JPT][hapmap]
rs3007708	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3791153	0.82[CHB][hapmap]
rs6587640	0.86[CHB][hapmap]
rs6678672	0.86[CHB][hapmap]
rs7541099	0.81[CHB][hapmap]
rs902313	0.81[CHB][hapmap]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2932570	S100A10	cis	multi-tissue	Pritchard
rs2932570	THEM4	cis	multi-tissue	Pritchard
rs2932570	NBPF18P	cis	Nerve Tibial	GTEx
rs2932570	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2932570	THEM4	cis	Esophagus Muscularis	GTEx
rs2932570	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2932570	S100A10	cis	Lymphoblastoid	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151976800-151993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151986200-151989800	Enhancers	HMEC	breast
3	chr1:151986400-151988200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:151986600-151987400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:151986600-151987600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151986600-151987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:151986600-151988000	Weak transcription	NHEK	skin
8	chr1:151986600-151996200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:151986800-151987600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:151986800-151988000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:151986800-151990000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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