Variant report

Variant	rs3740522
Chromosome Location	chr10:99019144-99019145
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	chr10:99019069..99020733-chr10:99024295..99026088,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10736115	0.91[CEU][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10736116	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10748691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs10748692	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10748694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786321	0.91[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10786323	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10786324	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10786326	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10786327	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10786329	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10786330	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10786332	0.83[EUR][1000 genomes]
rs10786333	0.82[EUR][1000 genomes]
rs10786335	0.80[EUR][1000 genomes]
rs10882881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10882883	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882889	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882890	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10882891	1.00[CEU][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882897	0.83[EUR][1000 genomes]
rs10882898	0.83[EUR][1000 genomes]
rs10882899	0.82[EUR][1000 genomes]
rs11189100	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11189120	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189122	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11189127	0.81[EUR][1000 genomes]
rs11189131	0.83[TSI][hapmap]
rs11189132	0.95[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs11189137	0.80[EUR][1000 genomes]
rs11189138	0.80[EUR][1000 genomes]
rs12221430	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12413688	0.81[EUR][1000 genomes]
rs12571098	0.80[EUR][1000 genomes]
rs1468069	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs1572437	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2065861	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2297987	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs2861875	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3740512	0.96[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs3781373	0.87[CEU][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs3814164	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs4917766	0.96[CEU][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4919087	1.00[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4919089	0.83[EUR][1000 genomes]
rs4919090	0.83[EUR][1000 genomes]
rs4919091	0.83[EUR][1000 genomes]
rs61863767	0.84[EUR][1000 genomes]
rs7067835	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7072078	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074678	0.85[LWK][hapmap];0.83[YRI][hapmap]
rs7076523	0.82[EUR][1000 genomes]
rs7078288	0.96[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7901853	0.82[CEU][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs945189	0.96[CEU][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3361060	chr10:98939103-99025202	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv1797410	chr10:98983785-99041740	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1040903	chr10:98986382-99047475	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3740522	EXOSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98977200-99023800	Weak transcription	Colonic Mucosa	Colon
2	chr10:98977400-99027000	Weak transcription	Right Ventricle	heart
3	chr10:98978600-99030400	Weak transcription	NH-A	brain
4	chr10:98978600-99037400	Weak transcription	HSMM	muscle
5	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:98979000-99027400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:98981400-99025400	Weak transcription	Colon Smooth Muscle	Colon
8	chr10:98982600-99020800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr10:98983000-99022000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:98983000-99027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:98983000-99027400	Weak transcription	Psoas Muscle	Psoas
12	chr10:98983000-99037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr10:98983200-99027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:98984600-99037600	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:98986800-99021200	Weak transcription	Hela-S3	cervix
16	chr10:98986800-99022600	Weak transcription	Spleen	Spleen
17	chr10:98986800-99027000	Weak transcription	Brain Angular Gyrus	brain
18	chr10:98986800-99027800	Weak transcription	Gastric	stomach
19	chr10:98987200-99029200	Weak transcription	HMEC	breast
20	chr10:98987200-99051200	Weak transcription	Pancreas	Pancrea
21	chr10:98988800-99027000	Weak transcription	Small Intestine	intestine
22	chr10:98988800-99028200	Weak transcription	Esophagus	oesophagus
23	chr10:98989000-99034600	Weak transcription	Aorta	Aorta
24	chr10:98989200-99029200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:98989600-99027200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr10:98989600-99038000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:98989800-99029800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:98990000-99034600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:98990400-99024400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:98994600-99039000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:98997600-99020400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:99003200-99026800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr10:99003400-99027200	Weak transcription	Brain Germinal Matrix	brain
34	chr10:99003800-99020800	Weak transcription	A549	lung
35	chr10:99003800-99021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:99003800-99028200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr10:99004000-99026000	Weak transcription	Brain Anterior Caudate	brain
38	chr10:99004000-99026400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr10:99004000-99027200	Weak transcription	Brain Substantia Nigra	brain
40	chr10:99004000-99028000	Weak transcription	NHDF-Ad	bronchial
41	chr10:99004400-99020600	Weak transcription	NHEK	skin
42	chr10:99004800-99037400	Weak transcription	Fetal Heart	heart
43	chr10:99005200-99046800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:99011600-99019800	Strong transcription	Fetal Thymus	thymus
45	chr10:99011800-99026200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr10:99012200-99025800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:99012400-99019400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr10:99012400-99019400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:99012600-99019400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:99012600-99019400	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links