Variant report

Variant	rs4917450
Chromosome Location	chr10:96009579-96009580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11187828	1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs11187830	0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12240281	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12248509	0.93[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12258052	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12262808	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12775991	0.88[ASN][1000 genomes]
rs12780278	0.87[ASN][1000 genomes]
rs1408820	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17109869	0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1830890	1.00[MEX][hapmap]
rs1969867	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2077218	0.83[CHD][hapmap]
rs2274225	0.96[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34775698	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34911703	0.87[ASN][1000 genomes]
rs35417689	0.92[ASN][1000 genomes]
rs35606681	0.92[ASN][1000 genomes]
rs36113000	0.90[ASN][1000 genomes]
rs4918172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4918182	0.96[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918184	0.96[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918188	1.00[MEX][hapmap]
rs61886339	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7072099	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7081879	0.94[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7083628	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7919066	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7919320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9787457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9787670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4917450	NOC3L	cis	parietal	SCAN
rs4917450	CYP2C18	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95973400-96012200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
3	chr10:95984800-96023800	Weak transcription	Pancreas	Pancrea
4	chr10:95985800-96033800	Weak transcription	Left Ventricle	heart
5	chr10:95986000-96011400	Weak transcription	Stomach Mucosa	stomach
6	chr10:95994600-96045400	Weak transcription	Lung	lung
7	chr10:95995800-96051800	Weak transcription	Fetal Kidney	kidney
8	chr10:96000800-96010200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr10:96004200-96015200	Weak transcription	Brain Substantia Nigra	brain
10	chr10:96004200-96022600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr10:96004400-96011200	Weak transcription	Placenta	Placenta
12	chr10:96004400-96034000	Weak transcription	Fetal Brain Male	brain
13	chr10:96005000-96016400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:96005000-96031200	Weak transcription	Brain Germinal Matrix	brain
15	chr10:96005200-96014200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:96005600-96019000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:96005800-96009600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:96005800-96009600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr10:96006000-96013600	Weak transcription	Right Ventricle	heart
20	chr10:96006400-96012000	Weak transcription	Spleen	Spleen
21	chr10:96006400-96012200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:96006400-96012200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:96006600-96010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:96006600-96010600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:96006600-96011000	Weak transcription	HSMMtube	muscle
26	chr10:96006600-96011800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr10:96006600-96012000	Weak transcription	Fetal Intestine Large	intestine
28	chr10:96006600-96012000	Weak transcription	Fetal Lung	lung
29	chr10:96006600-96012200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr10:96006600-96012200	Weak transcription	Adipose Nuclei	Adipose
31	chr10:96006600-96012400	Weak transcription	Aorta	Aorta
32	chr10:96006600-96012400	Weak transcription	Fetal Brain Female	brain
33	chr10:96006600-96012400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:96006600-96013000	Weak transcription	Colonic Mucosa	Colon
35	chr10:96006600-96030200	Weak transcription	Gastric	stomach
36	chr10:96006600-96030200	Weak transcription	Ovary	ovary
37	chr10:96006600-96033600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:96006800-96010800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:96006800-96011400	Weak transcription	A549	lung
40	chr10:96008000-96011200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:96008200-96010200	Strong transcription	Fetal Intestine Small	intestine
42	chr10:96008600-96022600	Strong transcription	Fetal Muscle Leg	muscle
43	chr10:96008800-96011400	Weak transcription	Fetal Stomach	stomach
44	chr10:96009000-96012000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr10:96009400-96024000	Weak transcription	Small Intestine	intestine

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