Variant report

Variant	rs62370646
Chromosome Location	chr5:42515027-42515028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42422660..42423547-chr5:42514575..42515445,3	MCF-7	breast:
2	chr5:42514982..42515546-chr5:42656463..42657052,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC152-7	chr5:42514969-42515114	NONHSAT101217

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10755268	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117110	0.88[EUR][1000 genomes]
rs11738365	0.87[EUR][1000 genomes]
rs11742495	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747975	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748366	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957616	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162973	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396768	0.85[EUR][1000 genomes]
rs1396773	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467049	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509452	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509453	1.00[ASN][1000 genomes]
rs1509455	0.85[EUR][1000 genomes]
rs1509456	0.85[EUR][1000 genomes]
rs1567374	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605851	0.88[EUR][1000 genomes]
rs1858136	0.85[EUR][1000 genomes]
rs1858137	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858139	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876788	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876790	0.85[EUR][1000 genomes]
rs1912107	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960498	0.88[EUR][1000 genomes]
rs2036745	0.90[EUR][1000 genomes]
rs2175126	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202883	0.87[EUR][1000 genomes]
rs2221712	0.87[EUR][1000 genomes]
rs2395970	0.88[EUR][1000 genomes]
rs2940912	0.85[EUR][1000 genomes]
rs2940914	0.88[EUR][1000 genomes]
rs2940916	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940917	0.90[EUR][1000 genomes]
rs2940918	0.90[EUR][1000 genomes]
rs2940919	0.85[EUR][1000 genomes]
rs2940920	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940922	0.90[EUR][1000 genomes]
rs2940926	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940929	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940931	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940934	0.88[EUR][1000 genomes]
rs2940935	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940939	0.83[EUR][1000 genomes]
rs2940942	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940943	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972391	1.00[ASN][1000 genomes]
rs2972395	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972400	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972404	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972406	0.86[EUR][1000 genomes]
rs2972407	0.88[EUR][1000 genomes]
rs2972410	0.90[EUR][1000 genomes]
rs2972411	0.90[EUR][1000 genomes]
rs2972412	0.90[EUR][1000 genomes]
rs2972413	0.90[EUR][1000 genomes]
rs2972414	0.85[EUR][1000 genomes]
rs2972415	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972416	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2972417	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972419	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509769	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642376	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866890	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58416991	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58960035	1.00[ASN][1000 genomes]
rs60126365	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61636452	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370642	1.00[ASN][1000 genomes]
rs62370648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451614	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881436	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884737	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7379192	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704355	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728337	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686286	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974051	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42508000-42516600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:42508200-42515200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:42509600-42516600	Weak transcription	Fetal Stomach	stomach
4	chr5:42510400-42516400	Weak transcription	Right Ventricle	heart
5	chr5:42513600-42515400	Enhancers	Liver	Liver
6	chr5:42514200-42515200	Enhancers	Right Atrium	heart
7	chr5:42514200-42515600	Enhancers	Fetal Heart	heart
8	chr5:42514200-42516000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:42514200-42516000	Enhancers	Psoas Muscle	Psoas
10	chr5:42514200-42516400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr5:42514200-42516400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:42514400-42515200	Weak transcription	Ovary	ovary
13	chr5:42514600-42515400	Enhancers	Fetal Muscle Leg	muscle
14	chr5:42514600-42515800	Strong transcription	Adipose Nuclei	Adipose
15	chr5:42514800-42515200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:42514800-42515600	Weak transcription	Aorta	Aorta
17	chr5:42514800-42516400	Weak transcription	Left Ventricle	heart
18	chr5:42514800-42516600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:42515000-42515400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr5:42515000-42515400	Enhancers	Fetal Lung	lung
21	chr5:42515000-42515600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr5:42515000-42515800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:42515000-42516000	Enhancers	Fetal Kidney	kidney
24	chr5:42515000-42516600	Enhancers	HepG2	liver
25	chr5:42515000-42517600	Enhancers	Fetal Intestine Large	intestine

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