Variant report

Variant	rs1830890
Chromosome Location	chr10:96019501-96019502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10786156	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs11187830	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11187838	0.80[AFR][1000 genomes]
rs12240281	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12258052	0.80[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs1408820	0.80[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17109869	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1858610	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969867	0.85[EUR][1000 genomes]
rs2274225	0.85[EUR][1000 genomes]
rs35443777	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740362	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4917450	1.00[MEX][hapmap]
rs4918182	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4918184	0.85[EUR][1000 genomes]
rs4918188	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55753709	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61886339	0.85[EUR][1000 genomes]
rs7072099	0.85[EUR][1000 genomes]
rs7072574	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7075045	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081879	0.82[EUR][1000 genomes]
rs7083628	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7919066	1.00[MEX][hapmap]
rs7919320	1.00[MEX][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1830890	NOC3L	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:95984800-96023800	Weak transcription	Pancreas	Pancrea
3	chr10:95985800-96033800	Weak transcription	Left Ventricle	heart
4	chr10:95994600-96045400	Weak transcription	Lung	lung
5	chr10:95995800-96051800	Weak transcription	Fetal Kidney	kidney
6	chr10:96004200-96022600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr10:96004400-96034000	Weak transcription	Fetal Brain Male	brain
8	chr10:96005000-96031200	Weak transcription	Brain Germinal Matrix	brain
9	chr10:96006600-96030200	Weak transcription	Gastric	stomach
10	chr10:96006600-96030200	Weak transcription	Ovary	ovary
11	chr10:96006600-96033600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr10:96008600-96022600	Strong transcription	Fetal Muscle Leg	muscle
13	chr10:96009400-96024000	Weak transcription	Small Intestine	intestine
14	chr10:96012600-96020600	Weak transcription	Fetal Lung	lung
15	chr10:96012600-96030600	Weak transcription	Stomach Mucosa	stomach
16	chr10:96012800-96019800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:96012800-96030600	Weak transcription	Spleen	Spleen
18	chr10:96013200-96034000	Weak transcription	Adipose Nuclei	Adipose
19	chr10:96013400-96019800	Weak transcription	Aorta	Aorta
20	chr10:96013600-96034000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr10:96014000-96030000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:96014000-96034000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:96014400-96030800	Weak transcription	Placenta	Placenta
24	chr10:96015000-96070200	Weak transcription	Fetal Brain Female	brain
25	chr10:96016800-96019800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr10:96016800-96032600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:96017000-96033600	Weak transcription	HSMMtube	muscle
28	chr10:96017800-96019800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:96017800-96021000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:96017800-96021000	Strong transcription	Fetal Intestine Small	intestine
31	chr10:96017800-96021200	Strong transcription	Fetal Stomach	stomach
32	chr10:96018000-96022600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:96018200-96020200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr10:96018200-96020200	Strong transcription	A549	lung
35	chr10:96018400-96020200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr10:96018400-96022600	Strong transcription	Fetal Intestine Large	intestine
37	chr10:96018400-96022800	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr10:96018800-96020200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr10:96019000-96020000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:96019000-96028000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr10:96019000-96028600	Weak transcription	Colonic Mucosa	Colon

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