Variant report

Variant	rs1051795
Chromosome Location	chr5:74896798-74896799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:15412992..15413653-chr5:74896234..74896879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148468	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10038723	0.88[EUR][1000 genomes]
rs10043621	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10044053	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060260	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10067641	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10075139	0.92[EUR][1000 genomes]
rs10434644	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462517	0.83[EUR][1000 genomes]
rs10474436	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10942739	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12234032	0.83[EUR][1000 genomes]
rs13354407	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1427924	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17739580	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1863934	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863935	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1995267	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253392	0.81[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs253393	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs253407	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs253408	0.86[ASN][1000 genomes]
rs253409	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2878519	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2878520	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34340	0.92[ASN][1000 genomes]
rs34344	0.84[ASN][1000 genomes]
rs34345	0.84[ASN][1000 genomes]
rs3761742	0.83[EUR][1000 genomes]
rs3846665	0.83[EUR][1000 genomes]
rs4045166	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4385188	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4440336	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4703674	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4704214	0.83[EUR][1000 genomes]
rs4704224	0.84[EUR][1000 genomes]
rs4704228	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57149337	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57312935	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744533	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744555	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5744575	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744595	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744621	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5744663	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744703	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59506842	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61430233	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67969809	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6861279	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6863398	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6872314	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6874781	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6886841	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891949	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs698912	0.83[EUR][1000 genomes]
rs73120833	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7445415	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767676	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7706857	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7709282	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7717505	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7723531	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924452	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9293656	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9332464	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885386	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv882198	chr5:74736065-74896798	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1051795	GCNT4	cis	cerebellum	SCAN
rs1051795	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74818200-74897400	Weak transcription	Thymus	Thymus
2	chr5:74833400-74906800	Weak transcription	Brain Substantia Nigra	brain
3	chr5:74839400-74897400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:74841200-74899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:74862200-74897800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:74862600-74897200	Weak transcription	Lung	lung
7	chr5:74862800-74897400	Weak transcription	Pancreas	Pancrea
8	chr5:74862800-74897400	Weak transcription	Spleen	Spleen
9	chr5:74862800-74897600	Weak transcription	Gastric	stomach
10	chr5:74862800-74907200	Weak transcription	Esophagus	oesophagus
11	chr5:74863600-74905800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:74863800-74906800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:74864000-74897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:74864000-74897400	Weak transcription	NHEK	skin
15	chr5:74864000-74899600	Weak transcription	Hela-S3	cervix
16	chr5:74864000-74907000	Weak transcription	Psoas Muscle	Psoas
17	chr5:74865800-74906800	Weak transcription	Colonic Mucosa	Colon
18	chr5:74867600-74907200	Weak transcription	Small Intestine	intestine
19	chr5:74871400-74897400	Weak transcription	Aorta	Aorta
20	chr5:74871400-74897400	Weak transcription	Brain Angular Gyrus	brain
21	chr5:74871400-74897400	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:74871400-74897400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:74871800-74900600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr5:74872400-74898400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:74873600-74907000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:74873800-74899200	Weak transcription	K562	blood
27	chr5:74873800-74901000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:74874600-74897400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:74875200-74907000	Weak transcription	Right Ventricle	heart
30	chr5:74875800-74903400	Weak transcription	Fetal Thymus	thymus
31	chr5:74877000-74898400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:74877400-74899200	Weak transcription	HUVEC	blood vessel
33	chr5:74878200-74899000	Weak transcription	HMEC	breast
34	chr5:74878400-74898200	Weak transcription	Fetal Brain Male	brain
35	chr5:74878600-74901200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:74879000-74907000	Weak transcription	HepG2	liver
37	chr5:74879600-74897800	Weak transcription	NHLF	lung
38	chr5:74881800-74896800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:74882400-74897000	Weak transcription	Fetal Lung	lung
40	chr5:74884600-74901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:74884800-74897200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:74884800-74897800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr5:74885000-74897800	Weak transcription	NH-A	brain
44	chr5:74885400-74901000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:74887800-74897400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:74889000-74897200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:74889200-74897400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:74889600-74897200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:74889800-74897200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:74889800-74897400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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