Variant report

Variant	rs10819718
Chromosome Location	chr9:102778480-102778481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10512269	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10760707	0.89[EUR][1000 genomes]
rs10760708	0.89[EUR][1000 genomes]
rs10760719	0.89[CEU][hapmap]
rs10819721	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs10819725	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10819726	0.88[CEU][hapmap]
rs10819727	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10819730	0.86[CEU][hapmap]
rs10819731	0.89[CEU][hapmap]
rs10819732	0.88[CEU][hapmap]
rs10988907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10988932	0.89[EUR][1000 genomes]
rs10988936	0.89[EUR][1000 genomes]
rs10988944	0.93[EUR][1000 genomes]
rs10988948	0.96[EUR][1000 genomes]
rs10988952	0.96[EUR][1000 genomes]
rs10988954	0.96[EUR][1000 genomes]
rs10988955	0.96[EUR][1000 genomes]
rs10988956	0.96[EUR][1000 genomes]
rs10988957	0.96[EUR][1000 genomes]
rs10988960	0.93[EUR][1000 genomes]
rs10988964	0.93[EUR][1000 genomes]
rs10988966	0.93[EUR][1000 genomes]
rs10988967	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10988972	0.93[EUR][1000 genomes]
rs10988977	0.89[CEU][hapmap]
rs10988978	0.89[CEU][hapmap]
rs10988982	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs10988984	0.89[CEU][hapmap]
rs10988988	0.89[CEU][hapmap]
rs10988989	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10988993	0.89[CEU][hapmap]
rs10988994	0.88[CEU][hapmap]
rs10988996	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10989003	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10989004	0.89[CEU][hapmap]
rs10989007	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10989010	0.89[CEU][hapmap]
rs10989013	0.89[CEU][hapmap]
rs10989017	0.89[CEU][hapmap]
rs10989018	0.80[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10989019	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs11515448	0.96[EUR][1000 genomes]
rs11789482	0.89[CEU][hapmap]
rs11794753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11998890	0.89[CEU][hapmap]
rs12377746	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs1415927	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs14297	1.00[GIH][hapmap]
rs1529195	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2416986	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs41305451	1.00[ASN][1000 genomes]
rs57875316	0.89[EUR][1000 genomes]
rs6479004	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7020150	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs7020780	0.89[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs7021923	0.89[CEU][hapmap]
rs7022643	0.96[EUR][1000 genomes]
rs7025271	0.89[CEU][hapmap]
rs7025412	0.88[CEU][hapmap]
rs7026341	0.96[EUR][1000 genomes]
rs7026529	0.96[EUR][1000 genomes]
rs7026567	0.89[CEU][hapmap]
rs7028564	0.89[CEU][hapmap]
rs7028939	0.94[EUR][1000 genomes]
rs7031081	0.82[EUR][1000 genomes]
rs7041818	0.89[CEU][hapmap]
rs7043946	0.96[EUR][1000 genomes]
rs7047193	0.88[CEU][hapmap]
rs7047693	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7350268	0.85[CEU][hapmap]
rs73505717	0.93[EUR][1000 genomes]
rs7849323	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7849609	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs7853497	0.89[CEU][hapmap]
rs7854689	0.89[CEU][hapmap]
rs7857556	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7858045	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7860268	0.89[CEU][hapmap]
rs7860660	0.89[CEU][hapmap]
rs7862614	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7865483	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7866669	0.89[CEU][hapmap]
rs7866950	0.89[CEU][hapmap]
rs7867803	0.96[EUR][1000 genomes]
rs7868020	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7868446	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7868632	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7870469	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7870701	1.00[CEU][hapmap]
rs7872897	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7873545	0.89[EUR][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	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10819718	INVS	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102729600-102826800	Weak transcription	HMEC	breast
2	chr9:102757400-102790600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:102760800-102783400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:102762000-102790000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:102763400-102783400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:102764200-102783200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:102766400-102783400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:102766400-102784600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:102766400-102785400	Weak transcription	Fetal Brain Male	brain
10	chr9:102766400-102787000	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:102766400-102794800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:102766600-102787200	Weak transcription	Psoas Muscle	Psoas
13	chr9:102766800-102783400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:102766800-102784600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr9:102766800-102793000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:102767000-102781400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:102767000-102783400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:102767000-102783400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:102767000-102783400	Weak transcription	NHEK	skin
20	chr9:102767000-102785200	Weak transcription	Brain Substantia Nigra	brain
21	chr9:102767000-102785400	Weak transcription	Brain Germinal Matrix	brain
22	chr9:102767000-102787800	Weak transcription	Right Ventricle	heart
23	chr9:102767000-102799400	Weak transcription	Spleen	Spleen
24	chr9:102767000-102820400	Weak transcription	Colonic Mucosa	Colon
25	chr9:102767200-102784800	Weak transcription	A549	lung
26	chr9:102767200-102789800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:102767200-102821800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:102767600-102781800	Weak transcription	HepG2	liver
29	chr9:102767600-102783400	Weak transcription	Lung	lung
30	chr9:102767600-102785800	Weak transcription	Pancreas	Pancrea
31	chr9:102767600-102788200	Weak transcription	Brain Angular Gyrus	brain
32	chr9:102767600-102790200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:102767600-102790400	Weak transcription	Brain Anterior Caudate	brain
34	chr9:102767600-102796000	Weak transcription	Gastric	stomach
35	chr9:102767600-102799400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:102767600-102800400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:102767600-102826400	Weak transcription	Small Intestine	intestine
38	chr9:102767600-102845600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:102767800-102778600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:102767800-102830000	Weak transcription	HSMMtube	muscle
41	chr9:102767800-102835600	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:102771400-102816200	Weak transcription	NH-A	brain
43	chr9:102771800-102783400	Weak transcription	Fetal Intestine Small	intestine
44	chr9:102772000-102779200	Strong transcription	Primary B cells from cord blood	blood
45	chr9:102773600-102787000	Weak transcription	Fetal Brain Female	brain
46	chr9:102774000-102779200	Strong transcription	K562	blood
47	chr9:102774000-102780800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:102774000-102784800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr9:102774000-102787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:102774000-102787600	Weak transcription	NHDF-Ad	bronchial

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