Variant report

Variant	rs980204
Chromosome Location	chr10:94716313-94716314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1033976	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10466167	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10736071	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10736072	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10748586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10786057	0.81[EUR][1000 genomes]
rs10882124	0.90[JPT][hapmap]
rs1097215	0.85[ASN][1000 genomes]
rs11187206	0.90[JPT][hapmap]
rs1326329	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326331	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1326332	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1409387	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1536329	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1536330	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1538648	1.00[JPT][hapmap]
rs2025730	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2094232	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2148361	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2182451	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2246370	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2246382	0.80[EUR][1000 genomes]
rs2250393	1.00[ASW][hapmap];0.92[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];0.81[EUR][1000 genomes]
rs2422072	0.93[GIH][hapmap];0.87[TSI][hapmap]
rs2478232	0.85[ASN][1000 genomes]
rs2486689	0.85[ASN][1000 genomes]
rs2486690	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2490732	0.81[EUR][1000 genomes]
rs2490733	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2490740	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes]
rs2490742	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes]
rs2497322	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs2497323	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes]
rs2497324	0.92[CEU][hapmap]
rs2497326	1.00[AFR][1000 genomes]
rs2497327	1.00[AFR][1000 genomes]
rs2497339	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2497348	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs4517429	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4919038	0.85[ASN][1000 genomes]
rs4933241	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4933242	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4933752	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6583846	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6583848	0.90[EUR][1000 genomes]
rs7069070	0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7070025	0.93[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7078376	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7082382	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7089179	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7477130	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893270	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7894145	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7897839	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7909191	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7909581	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7913340	0.84[CEU][hapmap];0.93[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs7914859	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7918909	0.90[JPT][hapmap]
rs835250	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835259	0.81[ASN][1000 genomes]
rs835267	0.81[ASN][1000 genomes]
rs860668	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9633695	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs973733	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv467435	chr10:94716313-94779550	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv551943	chr10:94716313-94779550	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs980204	NOC3L	cis	parietal	SCAN
rs980204	CEP55	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94652400-94717400	Weak transcription	Esophagus	oesophagus
2	chr10:94652600-94718000	Weak transcription	Ovary	ovary
3	chr10:94652600-94742400	Weak transcription	HSMMtube	muscle
4	chr10:94653200-94725200	Weak transcription	Fetal Lung	lung
5	chr10:94653400-94730200	Weak transcription	Fetal Brain Male	brain
6	chr10:94658000-94732400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:94658000-94750000	Weak transcription	Aorta	Aorta
8	chr10:94658600-94725800	Weak transcription	Lung	lung
9	chr10:94662600-94748400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:94667400-94733400	Weak transcription	Pancreas	Pancrea
11	chr10:94674800-94724600	Weak transcription	HSMM	muscle
12	chr10:94681000-94717000	Weak transcription	Brain Anterior Caudate	brain
13	chr10:94683400-94724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:94686600-94719600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:94687200-94718200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr10:94687400-94724200	Weak transcription	NHLF	lung
17	chr10:94689200-94738000	Weak transcription	Fetal Thymus	thymus
18	chr10:94689800-94724600	Weak transcription	A549	lung
19	chr10:94690000-94717600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr10:94690000-94730000	Weak transcription	Placenta	Placenta
21	chr10:94692200-94717800	Weak transcription	Brain Germinal Matrix	brain
22	chr10:94692800-94721800	Strong transcription	HUVEC	blood vessel
23	chr10:94692800-94724400	Weak transcription	Small Intestine	intestine
24	chr10:94699000-94717400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr10:94699200-94721600	Weak transcription	Fetal Intestine Large	intestine
26	chr10:94699400-94728600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr10:94699800-94722800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr10:94700000-94723000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr10:94700400-94722800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr10:94701400-94720600	Weak transcription	Fetal Kidney	kidney
31	chr10:94703000-94731800	Weak transcription	Spleen	Spleen
32	chr10:94704000-94718400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:94704400-94717800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:94704600-94731800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:94705600-94716400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:94706600-94731600	Weak transcription	Hela-S3	cervix
37	chr10:94706800-94717400	Strong transcription	Dnd41	blood
38	chr10:94707400-94735400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr10:94708200-94732400	Weak transcription	Colon Smooth Muscle	Colon
40	chr10:94709000-94721800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr10:94709000-94731800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr10:94709000-94735400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:94709400-94720000	Weak transcription	Right Ventricle	heart
44	chr10:94710400-94741400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr10:94711200-94730000	Weak transcription	K562	blood
46	chr10:94712200-94720600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:94712600-94787800	Weak transcription	Left Ventricle	heart
48	chr10:94713000-94716800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:94713000-94728800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:94713200-94720600	Weak transcription	Fetal Stomach	stomach

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