Variant report

Variant	rs3765524
Chromosome Location	chr10:96058298-96058299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10509670	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10509671	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs10786156	0.86[MKK][hapmap]
rs10786161	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882416	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882422	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882424	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882430	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882435	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10882436	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10882437	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882442	0.95[CEU][hapmap]
rs11187850	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187853	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187869	0.86[EUR][1000 genomes]
rs11187876	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187881	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187893	0.81[CEU][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11187894	0.83[EUR][1000 genomes]
rs11187899	0.83[EUR][1000 genomes]
rs11187900	0.83[EUR][1000 genomes]
rs11187901	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11558740	0.86[EUR][1000 genomes]
rs12217597	0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs12220125	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12263737	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12773229	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12780491	0.81[CEU][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs12781451	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2274223	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781264	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs3781265	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3818432	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6583934	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583935	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583937	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6583940	0.80[EUR][1000 genomes]
rs7074125	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7081265	0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7084339	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7084988	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7085378	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7092226	0.88[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7094783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7096037	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7099485	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7100430	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7100870	0.89[EUR][1000 genomes]
rs7897678	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897963	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7903902	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7908638	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914672	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers 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
4	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Esophageal cancer and gastric cancer	20729852	GWAS catalog
Dengue shock syndrome	22001756	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3765524	NOC3L	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96015000-96070200	Weak transcription	Fetal Brain Female	brain
2	chr10:96031800-96121000	Weak transcription	Stomach Mucosa	stomach
3	chr10:96035600-96066800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr10:96036000-96081600	Weak transcription	Left Ventricle	heart
5	chr10:96037800-96069000	Weak transcription	Gastric	stomach
6	chr10:96040200-96066200	Weak transcription	Pancreas	Pancrea
7	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
8	chr10:96045800-96061800	Weak transcription	Colonic Mucosa	Colon
9	chr10:96046200-96066200	Weak transcription	Right Atrium	heart
10	chr10:96047400-96060800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:96047800-96068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:96048800-96074800	Weak transcription	Placenta	Placenta
13	chr10:96049400-96081600	Weak transcription	Spleen	Spleen
14	chr10:96052800-96059000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr10:96052800-96073600	Weak transcription	Ovary	ovary
16	chr10:96053000-96058400	Weak transcription	Brain Anterior Caudate	brain
17	chr10:96053000-96059200	Weak transcription	HSMMtube	muscle
18	chr10:96053000-96068200	Weak transcription	Fetal Brain Male	brain
19	chr10:96053000-96083200	Weak transcription	Fetal Kidney	kidney
20	chr10:96053200-96081600	Weak transcription	Brain Substantia Nigra	brain
21	chr10:96053400-96058400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:96053400-96058400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:96053400-96058400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:96053400-96059200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:96053400-96066200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr10:96053400-96069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:96053400-96073000	Weak transcription	Fetal Lung	lung
28	chr10:96055200-96074600	Strong transcription	Fetal Muscle Leg	muscle
29	chr10:96055600-96058800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:96056800-96061400	Strong transcription	Fetal Intestine Small	intestine
31	chr10:96057200-96062200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr10:96057200-96066800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:96057600-96060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr10:96057600-96060600	Strong transcription	Fetal Intestine Large	intestine
35	chr10:96057800-96062000	Strong transcription	Fetal Stomach	stomach
36	chr10:96058000-96060400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr10:96058000-96060600	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr10:96058200-96058600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:96058200-96059000	Strong transcription	Adipose Nuclei	Adipose
40	chr10:96058200-96059000	Strong transcription	Aorta	Aorta
41	chr10:96058200-96059800	Strong transcription	A549	lung
42	chr10:96058200-96060200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:96058200-96060200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr10:96058200-96060400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:96058200-96060400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr10:96058200-96060400	Strong transcription	Stomach Smooth Muscle	stomach

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