Variant report

Variant	rs10508027
Chromosome Location	chr13:96590060-96590061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11616724	0.91[EUR][1000 genomes]
rs11618108	1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs11619636	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12428062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12430152	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1330556	0.95[ASN][1000 genomes]
rs1330557	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16951334	0.82[CHD][hapmap]
rs16951448	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1788062	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2129006	0.84[EUR][1000 genomes]
rs2170813	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3099362	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3099363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3101570	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4254181	0.95[ASN][1000 genomes]
rs4347496	0.90[ASN][1000 genomes]
rs4383020	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4409947	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4526890	0.95[ASN][1000 genomes]
rs4547219	1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs476954	0.82[AMR][1000 genomes]
rs4773932	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs492247	0.83[EUR][1000 genomes]
rs493423	0.89[EUR][1000 genomes]
rs495214	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs502311	0.84[EUR][1000 genomes]
rs504340	0.83[EUR][1000 genomes]
rs526702	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs531549	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs534010	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs534429	0.88[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs537463	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs539293	0.83[EUR][1000 genomes]
rs540213	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs56077337	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs565297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs565851	0.88[CEU][hapmap]
rs565898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs568170	0.89[EUR][1000 genomes]
rs581462	0.85[EUR][1000 genomes]
rs645595	1.00[JPT][hapmap]
rs651812	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs661544	0.86[ASN][1000 genomes]
rs662884	0.88[CEU][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs672988	0.84[EUR][1000 genomes]
rs674565	0.88[CEU][hapmap]
rs675144	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs688133	0.85[EUR][1000 genomes]
rs72636541	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72636556	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72636562	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72636570	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72637833	0.84[EUR][1000 genomes]
rs72637836	0.84[EUR][1000 genomes]
rs72637837	0.84[EUR][1000 genomes]
rs72637840	0.91[EUR][1000 genomes]
rs72638023	0.91[EUR][1000 genomes]
rs72638024	0.91[EUR][1000 genomes]
rs72638031	0.85[EUR][1000 genomes]
rs7323408	1.00[JPT][hapmap]
rs7331211	1.00[JPT][hapmap]
rs7331549	1.00[JPT][hapmap]
rs7332078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7334320	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7335209	1.00[ASN][1000 genomes]
rs7339059	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs7999737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000018	0.95[ASN][1000 genomes]
rs816122	0.85[EUR][1000 genomes]
rs816142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs9516621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs9525077	0.95[ASN][1000 genomes]
rs9525079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs9584324	1.00[JPT][hapmap]
rs9590344	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10508027	UGGT2	cis	cerebellum	SCAN
rs10508027	UGCGL2	cis	multi-tissue	Pritchard
rs10508027	DZIP1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96577000-96623200	Weak transcription	NHLF	lung
3	chr13:96577200-96598000	Weak transcription	HMEC	breast
4	chr13:96577800-96608800	Weak transcription	NHEK	skin
5	chr13:96584000-96599200	Weak transcription	Colonic Mucosa	Colon
6	chr13:96584200-96611000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:96584600-96592000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:96584600-96592200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:96584600-96592800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:96585000-96592600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:96585200-96592400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:96585800-96592200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:96586000-96601200	Weak transcription	NHDF-Ad	bronchial
14	chr13:96586200-96592400	Strong transcription	HSMM	muscle
15	chr13:96586400-96591600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr13:96586400-96592200	Strong transcription	Liver	Liver
17	chr13:96586600-96592200	Strong transcription	Adipose Nuclei	Adipose
18	chr13:96586600-96601400	Weak transcription	HUVEC	blood vessel
19	chr13:96586800-96590200	Weak transcription	Spleen	Spleen
20	chr13:96587200-96592200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr13:96587400-96592200	Strong transcription	Brain Cingulate Gyrus	brain
22	chr13:96587600-96592400	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr13:96587600-96592600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr13:96587800-96592200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr13:96588000-96592200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:96588200-96592200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr13:96588200-96592600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr13:96588200-96593000	Weak transcription	Fetal Brain Male	brain
29	chr13:96588400-96590200	Weak transcription	K562	blood
30	chr13:96588400-96591600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr13:96588400-96592600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:96588600-96592200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr13:96588600-96603400	Weak transcription	NH-A	brain
34	chr13:96588800-96590600	Weak transcription	Hela-S3	cervix
35	chr13:96588800-96592200	Strong transcription	Fetal Intestine Large	intestine
36	chr13:96588800-96596400	Weak transcription	Colon Smooth Muscle	Colon
37	chr13:96588800-96605400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:96588800-96606400	Weak transcription	Fetal Heart	heart
39	chr13:96588800-96611200	Weak transcription	Gastric	stomach
40	chr13:96589000-96590200	Weak transcription	Aorta	Aorta
41	chr13:96589000-96590200	Weak transcription	Psoas Muscle	Psoas
42	chr13:96589000-96590200	Weak transcription	Small Intestine	intestine
43	chr13:96589000-96590400	Weak transcription	Lung	lung
44	chr13:96589000-96590600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:96589000-96590600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:96589000-96590600	Weak transcription	Brain Angular Gyrus	brain
47	chr13:96589000-96590600	Weak transcription	Fetal Brain Female	brain
48	chr13:96589000-96590800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr13:96589000-96591000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr13:96589000-96591000	Weak transcription	Fetal Lung	lung

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