Variant report

Variant	rs6532795
Chromosome Location	chr4:100042221-100042222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10017466	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1042364	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1042365	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1126670	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1126671	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1126672	0.87[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1126673	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1139490	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1154401	0.81[CEU][hapmap]
rs1154405	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs1154410	0.87[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs1154412	0.93[GIH][hapmap]
rs11547772	0.82[LWK][hapmap]
rs1230154	0.96[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes]
rs1230155	0.87[GIH][hapmap]
rs1230156	0.84[AMR][1000 genomes]
rs1230157	0.93[GIH][hapmap]
rs1230164	0.88[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs1230165	0.86[GIH][hapmap]
rs13110176	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13110764	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13112176	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs1311615	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs1311616	0.88[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs1311617	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs13129488	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13133647	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13138294	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13143133	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs1377689	0.92[CEU][hapmap]
rs1453874	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs1540053	1.00[CHD][hapmap]
rs1573495	1.00[CHD][hapmap]
rs17217949	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17218003	0.87[CEU][hapmap]
rs17218073	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17218108	0.87[CEU][hapmap]
rs17218141	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs17218162	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs17218239	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17218288	0.87[CEU][hapmap]
rs17218560	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17218602	0.87[CEU][hapmap]
rs17817359	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17817868	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs17817958	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs1893881	1.00[CHD][hapmap]
rs1984362	0.83[CEU][hapmap]
rs1984364	0.83[CEU][hapmap]
rs2032349	1.00[CHD][hapmap]
rs2602865	0.80[EUR][1000 genomes]
rs2602866	0.80[EUR][1000 genomes]
rs2602872	0.81[EUR][1000 genomes]
rs2602876	0.81[EUR][1000 genomes]
rs2602877	0.82[EUR][1000 genomes]
rs2602878	0.82[EUR][1000 genomes]
rs2602881	0.84[EUR][1000 genomes]
rs2602882	0.83[EUR][1000 genomes]
rs2602883	0.84[EUR][1000 genomes]
rs2602888	0.84[EUR][1000 genomes]
rs2602891	0.82[EUR][1000 genomes]
rs2602893	0.82[EUR][1000 genomes]
rs2602894	0.81[EUR][1000 genomes]
rs2602895	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2602896	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2602897	0.81[EUR][1000 genomes]
rs2851246	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2851247	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2851248	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2851249	0.81[EUR][1000 genomes]
rs2851252	0.82[EUR][1000 genomes]
rs2851253	0.82[EUR][1000 genomes]
rs2851255	0.85[EUR][1000 genomes]
rs2851256	0.81[EUR][1000 genomes]
rs2851257	0.81[EUR][1000 genomes]
rs2851260	0.80[EUR][1000 genomes]
rs2851270	0.82[AMR][1000 genomes]
rs2851274	0.82[AMR][1000 genomes]
rs2851277	0.91[CEU][hapmap]
rs2851278	0.92[CEU][hapmap]
rs29001203	0.87[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs29001229	0.81[EUR][1000 genomes]
rs29001231	0.81[EUR][1000 genomes]
rs29001232	0.81[EUR][1000 genomes]
rs2924583	0.81[EUR][1000 genomes]
rs3018047	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs3018048	0.92[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs34936974	0.87[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs3919370	0.82[CEU][hapmap]
rs4141887	1.00[CHD][hapmap]
rs4235436	0.82[EUR][1000 genomes]
rs4699710	0.81[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4699712	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4699713	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs4699714	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs4699716	0.85[TSI][hapmap]
rs4699717	0.83[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs6532796	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6532798	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6532800	1.00[CHD][hapmap]
rs6822348	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6831352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6837685	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6848050	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6855482	1.00[CHD][hapmap]
rs7434491	0.83[CEU][hapmap]
rs7669636	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs7670060	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs7670241	0.87[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs7670638	0.81[CEU][hapmap]
rs7678936	1.00[CHD][hapmap]
rs7694646	0.86[CEU][hapmap]
rs9307234	1.00[CHD][hapmap]

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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6532795	ADH5	cis	Whole Blood	GTEx
rs6532795	ADH5	cis	parietal	SCAN
rs6532795	ADH5	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:100035000-100098200	Weak transcription	Ovary	ovary
4	chr4:100038800-100055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100040000-100043800	Weak transcription	Fetal Lung	lung
7	chr4:100040000-100045000	Weak transcription	Liver	Liver
8	chr4:100040000-100050800	Weak transcription	Fetal Intestine Large	intestine
9	chr4:100041000-100046400	Weak transcription	HepG2	liver
10	chr4:100041200-100042400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:100041200-100045000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:100041600-100042600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:100041600-100042600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:100041800-100042400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr4:100041800-100042400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:100042000-100042400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr4:100042000-100042600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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