Variant report

Variant	rs2932580
Chromosome Location	chr1:151934077-151934078
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151919533..151922319-chr1:151932817..151935606,2	MCF-7	breast:
2	chr1:151925413..151928425-chr1:151930738..151934740,3	MCF-7	breast:
3	chr1:151933684..151936159-chr1:151941486..151943210,2	MCF-7	breast:
4	chr1:151932606..151935514-chr1:151936511..151938848,2	MCF-7	breast:
5	chr1:151913842..151916280-chr1:151933238..151936084,3	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1038747	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10494270	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs11204915	0.81[CHB][hapmap]
rs11204919	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204920	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204922	0.82[CHB][hapmap]
rs11582739	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083193	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12095483	0.90[ASN][1000 genomes]
rs12116923	0.82[CHB][hapmap]
rs16833668	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833669	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833670	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833743	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1844543	0.88[ASN][1000 genomes]
rs1979637	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2279501	0.86[CHB][hapmap]
rs2279502	0.91[CHB][hapmap]
rs2337685	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2337686	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338019	0.86[CHB][hapmap]
rs2338206	0.85[ASN][1000 genomes]
rs28415528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932579	0.86[CHB][hapmap]
rs2932590	0.95[CHB][hapmap]
rs2999526	0.95[CHB][hapmap]
rs2999528	0.95[CHB][hapmap]
rs2999531	0.91[CHB][hapmap]
rs2999534	0.81[CHB][hapmap]
rs2999542	0.81[CHB][hapmap]
rs2999544	0.81[CHB][hapmap]
rs3007685	0.81[CHB][hapmap]
rs3007708	0.91[CHB][hapmap]
rs3007711	0.81[CHB][hapmap]
rs34251437	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3791153	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4845719	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56000812	0.85[ASN][1000 genomes]
rs56078223	0.85[ASN][1000 genomes]
rs56170235	0.85[ASN][1000 genomes]
rs56313205	0.86[ASN][1000 genomes]
rs57674198	0.85[ASN][1000 genomes]
rs57785325	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58087484	0.85[ASN][1000 genomes]
rs61814883	0.89[ASN][1000 genomes]
rs61817695	0.85[ASN][1000 genomes]
rs61817697	0.83[ASN][1000 genomes]
rs61817719	0.88[ASN][1000 genomes]
rs61817720	0.88[ASN][1000 genomes]
rs61817722	0.96[ASN][1000 genomes]
rs61817723	0.94[ASN][1000 genomes]
rs61817724	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61817725	0.96[ASN][1000 genomes]
rs6587632	0.88[ASN][1000 genomes]
rs6587633	0.88[ASN][1000 genomes]
rs6587634	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587640	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657658	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659662	0.83[ASN][1000 genomes]
rs6662602	0.96[ASN][1000 genomes]
rs6662611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662728	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663064	0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs6672064	0.84[ASN][1000 genomes]
rs6675930	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678672	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6682605	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684114	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686874	0.95[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs6691212	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693388	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693396	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693901	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695324	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701374	0.85[ASN][1000 genomes]
rs6703448	0.88[ASN][1000 genomes]
rs6703465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694840	0.86[ASN][1000 genomes]
rs7535002	0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7538652	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554832	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554859	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971887	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943221	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs9943251	0.82[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2932580	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2932580	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2932580	THEM4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151930800-151940800	Weak transcription	NHDF-Ad	bronchial
2	chr1:151931800-151935200	Weak transcription	Hela-S3	cervix
3	chr1:151932800-151934200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:151932800-151934200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:151932800-151934200	Enhancers	Stomach Mucosa	stomach
6	chr1:151932800-151936400	Enhancers	Fetal Kidney	kidney
7	chr1:151933000-151934200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:151933000-151934200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:151933000-151934400	Enhancers	Fetal Lung	lung
10	chr1:151933000-151934800	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:151933000-151934800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:151933200-151936200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:151933400-151934200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:151933400-151935600	Weak transcription	Adipose Nuclei	Adipose
15	chr1:151933400-151936400	Enhancers	NHEK	skin
16	chr1:151933600-151934800	Enhancers	Fetal Intestine Small	intestine
17	chr1:151933600-151937200	Enhancers	HUVEC	blood vessel
18	chr1:151933600-151945000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:151933800-151934200	Enhancers	Fetal Muscle Leg	muscle
20	chr1:151933800-151934200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:151933800-151934400	Enhancers	Duodenum Mucosa	Duodenum
22	chr1:151933800-151934800	Enhancers	Fetal Intestine Large	intestine
23	chr1:151934000-151934200	Enhancers	HSMM	muscle
24	chr1:151934000-151934600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:151934000-151934600	Enhancers	Psoas Muscle	Psoas
26	chr1:151934000-151940600	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links