Variant report

Variant	rs2932590
Chromosome Location	chr1:151953763-151953764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151953443..151955255-chr1:151956966..151958733,2	K562	blood:
2	chr1:151881739..151884643-chr1:151951894..151953889,2	K562	blood:
3	chr1:151952034..151953973-chr1:152006565..152009947,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1038747	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10494270	0.85[CHB][hapmap]
rs10788817	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10788820	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11204915	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap]
rs11204922	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11542015	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11589720	0.87[ASN][1000 genomes]
rs12083193	0.91[CHB][hapmap];0.82[TSI][hapmap]
rs12116923	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13320	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1387833	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1532133	0.86[CHB][hapmap]
rs16833668	0.91[CHB][hapmap]
rs16833728	0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs16833743	0.91[CHB][hapmap]
rs1979637	0.81[CHB][hapmap]
rs2279501	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2279502	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs2337689	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2338019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932570	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932574	0.82[ASN][1000 genomes]
rs2932579	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2932581	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932583	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2932586	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999508	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999512	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2999526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999534	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]
rs2999539	0.83[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2999542	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs2999544	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2999560	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2999561	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3007670	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3007685	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3007691	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007708	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007711	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs3791153	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs4845713	0.84[CHB][hapmap]
rs6587635	0.95[CHB][hapmap]
rs6587636	0.95[CHB][hapmap]
rs6587637	0.90[CHB][hapmap]
rs6587638	0.95[CHB][hapmap]
rs6587640	0.91[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap];0.86[TSI][hapmap]
rs6662611	0.95[CHB][hapmap]
rs6663064	0.91[CHB][hapmap];0.80[TSI][hapmap]
rs6678672	0.91[CHB][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap]
rs6685187	0.81[TSI][hapmap]
rs6686874	0.91[CHB][hapmap];0.80[TSI][hapmap]
rs6703465	0.95[CHB][hapmap]
rs7535002	0.91[CHB][hapmap]
rs7541099	0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs902313	0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs971887	0.95[CHB][hapmap];0.80[GIH][hapmap];0.86[TSI][hapmap]
rs9943221	0.86[CHB][hapmap];0.80[TSI][hapmap]
rs9943251	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2932590	THEM4	cis	uninvolved skin	skin_eQTL
rs2932590	S100A10	cis	cerebellum	SCAN
rs2932590	S100A10	cis	Lymphoblastoid	GTEx
rs2932590	SCNM1	cis	parietal	SCAN
rs2932590	THEM4	cis	parietal	SCAN
rs2932590	THEM4	cis	multi-tissue	Pritchard
rs2932590	THEM4	cis	Esophagus Muscularis	GTEx
rs2932590	S100A10	cis	lymphoblastoid	seeQTL
rs2932590	THEM4	cis	lymphoblastoid	seeQTL
rs2932590	THEM4	cis	cerebellum	SCAN
rs2932590	THEM4	cis	Nerve Tibial	GTEx
rs2932590	S100A10	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
5	chr1:151945600-151953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:151945600-151953800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:151946000-151954800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:151946000-151954800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:151946200-151954800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:151946200-151954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:151946200-151956200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:151946600-151957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:151946600-151958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:151948000-151956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:151948400-151955200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:151949200-151963200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:151949800-151954800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:151949800-151957200	Weak transcription	Stomach Mucosa	stomach
19	chr1:151950000-151956600	Genic enhancers	A549	lung
20	chr1:151950400-151953800	Weak transcription	Right Ventricle	heart
21	chr1:151950600-151954800	Weak transcription	Small Intestine	intestine
22	chr1:151950800-151954000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:151951000-151961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:151951200-151954800	Weak transcription	HepG2	liver
25	chr1:151951400-151954000	Enhancers	Placenta	Placenta
26	chr1:151951600-151953800	Weak transcription	Thymus	Thymus
27	chr1:151951600-151960800	Weak transcription	Fetal Thymus	thymus
28	chr1:151951800-151961800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:151952400-151954000	Enhancers	Colon Smooth Muscle	Colon
30	chr1:151952400-151954000	Enhancers	Right Atrium	heart
31	chr1:151952400-151954000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:151952400-151954000	Enhancers	HSMMtube	muscle
33	chr1:151952400-151954000	Enhancers	NH-A	brain
34	chr1:151952400-151959600	Genic enhancers	NHDF-Ad	bronchial
35	chr1:151952400-151960800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:151952600-151954000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:151952600-151954200	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr1:151952600-151954600	Strong transcription	Fetal Stomach	stomach
39	chr1:151952600-151957800	Genic enhancers	Fetal Intestine Small	intestine
40	chr1:151952600-151960400	Genic enhancers	NHEK	skin
41	chr1:151952800-151954000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:151952800-151954000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:151952800-151954000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:151952800-151954000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:151952800-151954000	Genic enhancers	Fetal Muscle Leg	muscle
46	chr1:151952800-151954000	Enhancers	Ovary	ovary
47	chr1:151952800-151954000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:151952800-151955000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:151952800-151955400	Genic enhancers	HMEC	breast
50	chr1:151952800-151956200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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