Variant report

Variant	rs2274223
Chromosome Location	chr10:96066341-96066342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:96065535..96067850-chr10:96072045..96074764,2	K562	blood:
2	chr10:96066295..96067881-chr10:96069190..96071900,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10509670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509671	0.83[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10786161	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10882416	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882422	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882424	0.82[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882430	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882437	0.82[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes]
rs11187850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187851	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11187853	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11187876	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187881	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11187893	0.93[MEX][hapmap]
rs11187901	0.82[ASW][hapmap];0.83[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes]
rs12217597	0.93[MEX][hapmap]
rs12220125	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12263737	0.87[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];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773229	0.81[AMR][1000 genomes]
rs12780491	0.93[MEX][hapmap]
rs3765524	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	0.83[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3781265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818432	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6583934	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6583935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6583937	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7074125	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7081265	0.86[MEX][hapmap]
rs7084339	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7084988	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7085378	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7092226	0.82[ASW][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap]
rs7094783	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7096037	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7096678	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7099485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100430	0.82[ASW][hapmap];0.82[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes]
rs7897678	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7897963	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7903902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7908638	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7914672	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Esophageal cancer	21642993	GWAS catalog
Esophageal squamous cell carcinoma	25129146	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2274223	NOC3L	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
7	chr10:96047800-96068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:96048800-96074800	Weak transcription	Placenta	Placenta
9	chr10:96049400-96081600	Weak transcription	Spleen	Spleen
10	chr10:96052800-96073600	Weak transcription	Ovary	ovary
11	chr10:96053000-96068200	Weak transcription	Fetal Brain Male	brain
12	chr10:96053000-96083200	Weak transcription	Fetal Kidney	kidney
13	chr10:96053200-96081600	Weak transcription	Brain Substantia Nigra	brain
14	chr10:96053400-96069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr10:96053400-96073000	Weak transcription	Fetal Lung	lung
16	chr10:96055200-96074600	Strong transcription	Fetal Muscle Leg	muscle
17	chr10:96057200-96066800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:96059000-96074800	Weak transcription	Adipose Nuclei	Adipose
19	chr10:96059400-96083200	Weak transcription	Brain Anterior Caudate	brain
20	chr10:96059600-96066600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr10:96059600-96081600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr10:96059800-96066600	Weak transcription	A549	lung
23	chr10:96059800-96067800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr10:96060000-96074800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:96060200-96066400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:96063200-96068200	Weak transcription	Colonic Mucosa	Colon
27	chr10:96063600-96076600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr10:96064200-96070600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:96064400-96068600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr10:96064400-96069400	Strong transcription	Fetal Intestine Large	intestine
31	chr10:96064400-96073800	Strong transcription	Fetal Stomach	stomach
32	chr10:96064600-96069000	Weak transcription	HepG2	liver
33	chr10:96064600-96069800	Strong transcription	Fetal Intestine Small	intestine
34	chr10:96064800-96070000	Weak transcription	Liver	Liver
35	chr10:96064800-96071600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr10:96064800-96072600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:96065200-96066400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr10:96066000-96067600	Strong transcription	Aorta	Aorta
39	chr10:96066000-96074800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr10:96066200-96067400	Strong transcription	Pancreas	Pancrea
41	chr10:96066200-96067800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr10:96066200-96071000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr10:96066200-96071800	Strong transcription	HSMMtube	muscle
44	chr10:96066200-96074800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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