Variant report

Variant	rs2999534
Chromosome Location	chr1:151976070-151976071
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151907075..151908631-chr1:151973771..151976149,2	MCF-7	breast:
2	chr1:151880825..151882446-chr1:151974960..151977633,2	K562	blood:
3	chr1:151879997..151882325-chr1:151975828..151977633,2	K562	blood:
4	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
5	chr1:151974328..151976089-chr1:152021628..152023753,2	MCF-7	breast:
6	chr1:151974357..151976309-chr1:151981505..151984353,2	K562	blood:
7	chr1:151974500..151976587-chr20:47516421..47517941,2	MCF-7	breast:
8	chr1:151879750..151883668-chr1:151974501..151979582,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1038747	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs10788820	0.81[JPT][hapmap]
rs11204915	0.81[MEX][hapmap]
rs11204922	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11542015	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12083193	0.86[CHB][hapmap];0.85[TSI][hapmap]
rs12116923	0.85[JPT][hapmap]
rs12410789	0.84[ASN][1000 genomes]
rs13320	0.81[MEX][hapmap]
rs1532133	1.00[CHB][hapmap]
rs16833728	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs16833743	0.86[CHB][hapmap]
rs1979637	0.95[CHB][hapmap]
rs1994606	0.81[ASN][1000 genomes]
rs2279501	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2279502	0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2338019	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932574	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932590	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999512	0.83[AMR][1000 genomes]
rs2999526	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999528	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2999531	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999539	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2999560	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999561	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007708	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791153	0.86[CHB][hapmap]
rs6587635	0.81[CHB][hapmap]
rs6587636	0.81[CHB][hapmap]
rs6587640	0.86[CHB][hapmap];0.85[TSI][hapmap]
rs6662611	0.81[CHB][hapmap]
rs6678672	0.86[CHB][hapmap];0.83[TSI][hapmap]
rs6685187	0.80[MEX][hapmap]
rs6703465	0.81[CHB][hapmap]
rs7541099	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs902313	0.81[CHB][hapmap];0.85[TSI][hapmap]
rs971887	0.81[CHB][hapmap];0.85[TSI][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2999534	LCE2C	cis	cerebellum	SCAN
rs2999534	S100A10	cis	multi-tissue	Pritchard
rs2999534	S100A10	cis	cerebellum	SCAN
rs2999534	ADAMTSL4	cis	cerebellum	SCAN
rs2999534	THEM4	cis	cerebellum	SCAN
rs2999534	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999534	S100A10	cis	parietal	SCAN
rs2999534	S100A10	cis	lymphoblastoid	seeQTL
rs2999534	THEM4	cis	uninvolved skin	skin_eQTL
rs2999534	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999534	MCL1	cis	cerebellum	SCAN
rs2999534	SLC18A3	trans	cerebellum	SCAN
rs2999534	THEM4	cis	Esophagus Muscularis	GTEx
rs2999534	THEM4	cis	parietal	SCAN
rs2999534	THEM4	cis	multi-tissue	Pritchard
rs2999534	S100A10	cis	Lymphoblastoid	GTEx
rs2999534	THEM4	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151966800-151976800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151967000-151977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:151967200-151977000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:151967800-151977200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:151973000-151976800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:151973200-151976200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:151974200-151976400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:151974200-151976400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:151974200-151976400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:151974200-151976600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:151974200-151977200	Enhancers	NHEK	skin
12	chr1:151974400-151976200	Weak transcription	Stomach Mucosa	stomach
13	chr1:151974400-151976800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:151974800-151976600	Enhancers	HMEC	breast
15	chr1:151975000-151976400	Weak transcription	Hela-S3	cervix
16	chr1:151975400-151976400	Enhancers	HSMMtube	muscle
17	chr1:151975600-151977200	Enhancers	Esophagus	oesophagus
18	chr1:151975600-151977200	Enhancers	Left Ventricle	heart
19	chr1:151975800-151977200	Enhancers	Fetal Heart	heart
20	chr1:151975800-151977200	Enhancers	Right Atrium	heart
21	chr1:151976000-151978400	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links