Variant report

Variant	rs7089179
Chromosome Location	chr10:94705357-94705358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1033976	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466167	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736071	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736072	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10748586	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786057	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326329	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1326331	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326332	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409387	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536329	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1536330	0.84[EUR][1000 genomes]
rs2025730	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094232	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148361	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182451	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246370	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246382	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246701	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250393	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422070	1.00[ASN][1000 genomes]
rs2422072	0.83[CEU][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs2488062	1.00[ASN][1000 genomes]
rs2490732	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490733	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490740	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490742	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490744	1.00[ASN][1000 genomes]
rs2497322	0.96[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs2497323	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2497324	0.96[CEU][hapmap];1.00[ASN][1000 genomes]
rs2497326	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2497327	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2497331	1.00[ASN][1000 genomes]
rs2497339	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497348	0.96[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs2497350	1.00[ASN][1000 genomes]
rs4517429	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933241	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933242	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933749	1.00[ASN][1000 genomes]
rs4933752	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583846	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583848	0.93[EUR][1000 genomes]
rs7069070	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs7070025	0.83[CEU][hapmap];0.96[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078376	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082382	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477130	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7893270	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894145	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897839	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7909191	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913340	0.88[CEU][hapmap];0.96[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914859	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835250	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860668	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9419746	1.00[ASN][1000 genomes]
rs9633695	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973733	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980204	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv895898	chr10:94628274-94810665	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1039261	chr10:94659515-94706633	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv515937	chr10:94660133-94725508	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv518124	chr10:94660133-94778283	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv522103	chr10:94660133-94810665	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv467434	chr10:94668524-94725508	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv551940	chr10:94668524-94725508	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv551941	chr10:94670849-94782735	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv551942	chr10:94695617-94810665	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7089179	CEP55	cis	cerebellum	SCAN
rs7089179	NOC3L	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94652400-94717400	Weak transcription	Esophagus	oesophagus
2	chr10:94652600-94712400	Weak transcription	Brain Angular Gyrus	brain
3	chr10:94652600-94718000	Weak transcription	Ovary	ovary
4	chr10:94652600-94742400	Weak transcription	HSMMtube	muscle
5	chr10:94652800-94706600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:94653200-94725200	Weak transcription	Fetal Lung	lung
7	chr10:94653400-94730200	Weak transcription	Fetal Brain Male	brain
8	chr10:94654600-94714600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:94658000-94732400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:94658000-94750000	Weak transcription	Aorta	Aorta
11	chr10:94658600-94725800	Weak transcription	Lung	lung
12	chr10:94662600-94748400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:94664600-94714600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:94667400-94733400	Weak transcription	Pancreas	Pancrea
15	chr10:94672000-94716000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:94674800-94724600	Weak transcription	HSMM	muscle
17	chr10:94675000-94708600	Weak transcription	K562	blood
18	chr10:94676400-94706400	Weak transcription	Thymus	Thymus
19	chr10:94679400-94706200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr10:94680600-94712800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:94680800-94708000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr10:94681000-94707600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:94681000-94717000	Weak transcription	Brain Anterior Caudate	brain
24	chr10:94683400-94724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:94686600-94719600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:94687200-94718200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr10:94687400-94724200	Weak transcription	NHLF	lung
28	chr10:94687600-94713200	Weak transcription	Brain Substantia Nigra	brain
29	chr10:94689200-94706800	Weak transcription	Left Ventricle	heart
30	chr10:94689200-94710400	Weak transcription	Psoas Muscle	Psoas
31	chr10:94689200-94738000	Weak transcription	Fetal Thymus	thymus
32	chr10:94689400-94706800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:94689400-94710400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:94689800-94706800	Weak transcription	Liver	Liver
35	chr10:94689800-94714800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:94689800-94724600	Weak transcription	A549	lung
37	chr10:94690000-94707800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:94690000-94717600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:94690000-94730000	Weak transcription	Placenta	Placenta
40	chr10:94691600-94706400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr10:94692200-94717800	Weak transcription	Brain Germinal Matrix	brain
42	chr10:94692800-94721800	Strong transcription	HUVEC	blood vessel
43	chr10:94692800-94724400	Weak transcription	Small Intestine	intestine
44	chr10:94694400-94714600	Weak transcription	HepG2	liver
45	chr10:94694600-94705800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr10:94696800-94712200	Weak transcription	Fetal Muscle Leg	muscle
47	chr10:94698800-94707000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr10:94699000-94708400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr10:94699000-94717400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr10:94699200-94721600	Weak transcription	Fetal Intestine Large	intestine

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