Variant report

Variant	rs4919089
Chromosome Location	chr10:99087905-99087906
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	chr10:99050766..99052270-chr10:99085293..99087979,2	MCF-7	breast:
2	chr10:99086397..99088974-chr10:99118500..99121306,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10736115	0.87[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs10736116	0.86[EUR][1000 genomes]
rs10748691	0.96[CEU][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10748692	0.80[EUR][1000 genomes]
rs10748694	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs10786321	0.87[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs10786324	0.87[EUR][1000 genomes]
rs10786325	0.82[EUR][1000 genomes]
rs10786326	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786327	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10786329	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786330	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786332	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10786333	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10786334	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786335	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882881	0.96[CEU][hapmap]
rs10882883	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10882884	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs10882889	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10882891	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882894	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10882895	0.82[ASN][1000 genomes]
rs10882897	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882899	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189100	0.82[EUR][1000 genomes]
rs11189120	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189122	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189127	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11189131	0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11189132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189137	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189138	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12221430	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12413688	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571098	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1334892	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1468069	0.91[CEU][hapmap]
rs1890966	0.98[ASN][1000 genomes]
rs2065861	0.85[CEU][hapmap]
rs2297987	0.91[CEU][hapmap]
rs2861875	0.96[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs3740512	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740522	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs3781373	0.91[CEU][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3814164	0.96[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs4917766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919087	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4919090	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919091	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61863767	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584116	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7067835	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7072078	0.83[EUR][1000 genomes]
rs7076523	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7080275	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7089634	0.82[EUR][1000 genomes]
rs7901853	0.87[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs945187	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs945189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.99[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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats 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
5	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv825534	chr10:99081505-99115599	Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4919089	C10orf62	cis	cerebellum	SCAN
rs4919089	EXOSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99080600-99091200	Weak transcription	HMEC	breast
2	chr10:99080800-99089800	Weak transcription	Dnd41	blood
3	chr10:99081200-99088000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:99081200-99091200	Weak transcription	Psoas Muscle	Psoas
5	chr10:99081200-99092600	Weak transcription	Aorta	Aorta
6	chr10:99081400-99088200	Weak transcription	Lung	lung
7	chr10:99081400-99088400	Weak transcription	Right Atrium	heart
8	chr10:99081400-99088800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:99081400-99089000	Weak transcription	Ovary	ovary
10	chr10:99081400-99089800	Weak transcription	Gastric	stomach
11	chr10:99081600-99088400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr10:99081600-99089000	Weak transcription	Esophagus	oesophagus
13	chr10:99081600-99091000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:99081600-99091600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr10:99081600-99091600	Weak transcription	Fetal Kidney	kidney
16	chr10:99081600-99091600	Weak transcription	HSMMtube	muscle
17	chr10:99081800-99088400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:99081800-99088600	Weak transcription	Colon Smooth Muscle	Colon
19	chr10:99081800-99091000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:99081800-99091000	Weak transcription	HUVEC	blood vessel
21	chr10:99081800-99091200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:99081800-99091200	Weak transcription	Small Intestine	intestine
23	chr10:99081800-99091200	Weak transcription	HSMM	muscle
24	chr10:99081800-99091800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:99081800-99092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:99081800-99092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:99082000-99088400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:99082000-99089800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr10:99082000-99089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:99082000-99091000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:99082000-99091000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:99082000-99091200	Weak transcription	Placenta	Placenta
33	chr10:99082200-99088600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr10:99082200-99088800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr10:99082200-99091200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:99082200-99091600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:99082400-99088200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr10:99082400-99088200	Weak transcription	Spleen	Spleen
39	chr10:99082400-99088400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:99082400-99088400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:99082400-99088400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr10:99082400-99088600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr10:99082400-99088600	Weak transcription	Brain Angular Gyrus	brain
44	chr10:99082400-99088800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:99082400-99089800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr10:99082400-99090000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr10:99082400-99090800	Weak transcription	Fetal Brain Male	brain
48	chr10:99082400-99091200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr10:99082800-99088200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:99082800-99088800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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