Variant report

Variant	rs1408820
Chromosome Location	chr10:96013824-96013825
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	0.90[LWK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs11187830	0.80[CHD][hapmap];1.00[MEX][hapmap]
rs12240281	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12248509	0.90[LWK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs12258052	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12262808	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs17109869	0.80[CHD][hapmap];1.00[MEX][hapmap]
rs1830890	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]
rs1858610	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1969867	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2077218	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2274225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34775698	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35443777	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3740362	0.84[EUR][1000 genomes]
rs4917450	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]
rs4918172	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4918182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918184	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4918188	0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs55753709	0.85[EUR][1000 genomes]
rs61886339	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7072099	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7072574	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7075045	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7081879	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7083628	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7919066	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[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];0.87[ASN][1000 genomes]
rs7919320	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9787457	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9787670	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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
rs1408820	TMEM20	cis	parietal	SCAN
rs1408820	NOC3L	cis	parietal	SCAN

Chromatin state (count:43 , 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	chr10:96004200-96015200	Weak transcription	Brain Substantia Nigra	brain
7	chr10:96004200-96022600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr10:96004400-96034000	Weak transcription	Fetal Brain Male	brain
9	chr10:96005000-96016400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr10:96005000-96031200	Weak transcription	Brain Germinal Matrix	brain
11	chr10:96005200-96014200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:96005600-96019000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:96006600-96030200	Weak transcription	Gastric	stomach
14	chr10:96006600-96030200	Weak transcription	Ovary	ovary
15	chr10:96006600-96033600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:96008600-96022600	Strong transcription	Fetal Muscle Leg	muscle
17	chr10:96009400-96024000	Weak transcription	Small Intestine	intestine
18	chr10:96009600-96018800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:96010600-96014800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr10:96010600-96014800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr10:96010800-96017200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr10:96011200-96014400	Strong transcription	Placenta	Placenta
23	chr10:96011200-96016800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:96011400-96015000	Strong transcription	Fetal Stomach	stomach
25	chr10:96011800-96015200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr10:96012000-96016000	Strong transcription	Fetal Intestine Small	intestine
27	chr10:96012000-96016800	Strong transcription	Fetal Intestine Large	intestine
28	chr10:96012000-96016800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr10:96012200-96014000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:96012200-96014000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:96012200-96015000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:96012400-96014800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:96012400-96015000	Strong transcription	Fetal Brain Female	brain
34	chr10:96012600-96020600	Weak transcription	Fetal Lung	lung
35	chr10:96012600-96030600	Weak transcription	Stomach Mucosa	stomach
36	chr10:96012800-96014200	Strong transcription	HSMMtube	muscle
37	chr10:96012800-96019800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:96012800-96030600	Weak transcription	Spleen	Spleen
39	chr10:96013000-96014800	Strong transcription	Colonic Mucosa	Colon
40	chr10:96013200-96014000	Weak transcription	A549	lung
41	chr10:96013200-96034000	Weak transcription	Adipose Nuclei	Adipose
42	chr10:96013400-96019800	Weak transcription	Aorta	Aorta
43	chr10:96013600-96034000	Weak transcription	Rectal Smooth Muscle	rectum

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