Variant report

Variant	rs2199545
Chromosome Location	chr8:118988162-118988163
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	chr8:118976562..118978924-chr8:118986229..118989159,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10087446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10097196	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10102745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10105797	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10955846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1125103	0.87[CEU][hapmap]
rs11780699	0.87[CEU][hapmap]
rs11781153	0.83[CEU][hapmap];0.84[CHD][hapmap]
rs11781245	0.87[CEU][hapmap]
rs13256042	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13260665	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1462985	0.84[JPT][hapmap]
rs1466429	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542519	0.83[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap]
rs1564132	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2168667	0.84[JPT][hapmap]
rs2219724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325820	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325821	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2447535	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2447536	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2447537	0.87[CEU][hapmap]
rs2447538	0.84[JPT][hapmap]
rs2447539	0.84[JPT][hapmap]
rs2447540	0.83[CEU][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap]
rs2447541	0.83[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs2514719	0.91[CEU][hapmap]
rs2514720	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs2514727	0.93[ASN][1000 genomes]
rs3101574	0.87[CEU][hapmap]
rs4298514	0.87[CEU][hapmap];0.87[GIH][hapmap]
rs4541958	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs4876774	0.83[CEU][hapmap]
rs4876775	0.83[CEU][hapmap]
rs4876777	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4876781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876784	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6469718	0.87[CEU][hapmap]
rs7815972	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7818831	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7840309	1.00[ASW][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs7843515	0.82[CHD][hapmap]
rs958381	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs9643120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv831440	chr8:118871930-119052269	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1032355	chr8:118896733-119003223	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1015380	chr8:118948652-119418389	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv539736	chr8:118948652-119418389	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1025002	chr8:118970940-119069418	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2199545	MAL2	cis	cerebellum	SCAN
rs2199545	NOV	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118970400-118989800	Weak transcription	HSMMtube	muscle
2	chr8:118970800-118989000	Weak transcription	HUVEC	blood vessel
3	chr8:118971600-118993000	Weak transcription	Psoas Muscle	Psoas
4	chr8:118971800-118989000	Weak transcription	Ovary	ovary
5	chr8:118972000-118989600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:118972200-118989600	Weak transcription	HSMM	muscle
7	chr8:118972200-118997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:118975400-118992400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:118976600-118991000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr8:118976800-118988600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr8:118978200-118992000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:118978600-118993000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr8:118979000-118991000	Weak transcription	HepG2	liver
14	chr8:118981200-118990200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr8:118981200-118992400	Weak transcription	Left Ventricle	heart
16	chr8:118982000-118993800	Weak transcription	Gastric	stomach
17	chr8:118982200-118992200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr8:118982400-118990000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr8:118982400-118992000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr8:118982600-118989800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:118983400-118993000	Weak transcription	Esophagus	oesophagus
22	chr8:118983600-118988600	Weak transcription	NH-A	brain
23	chr8:118983600-119000800	Weak transcription	Pancreas	Pancrea
24	chr8:118983800-118992200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr8:118983800-118992600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr8:118984000-118989600	Weak transcription	HMEC	breast
27	chr8:118984000-118989800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:118984200-118990200	Weak transcription	Small Intestine	intestine
29	chr8:118984200-118993600	Weak transcription	Fetal Intestine Large	intestine
30	chr8:118984800-118990400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr8:118985400-118990000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:118985600-118990800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr8:118986400-118989200	Enhancers	Aorta	Aorta
34	chr8:118986600-118988600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:118986600-118993000	Enhancers	NHLF	lung
36	chr8:118986800-118988200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:118986800-118988400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:118986800-118989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr8:118986800-118991200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr8:118987000-118988400	Enhancers	Fetal Lung	lung
41	chr8:118987000-118989000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:118987000-118989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr8:118987000-118989400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr8:118987000-118989800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:118987000-118990000	Enhancers	NHDF-Ad	bronchial
46	chr8:118987000-118993600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr8:118987200-118988200	Enhancers	Liver	Liver
48	chr8:118987200-118988800	Enhancers	NHEK	skin
49	chr8:118987200-118992200	Weak transcription	Lung	lung
50	chr8:118987200-118992200	Weak transcription	Spleen	Spleen

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