Variant report

Variant	rs3781264
Chromosome Location	chr10:96070375-96070376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:96068803..96071530-chr10:96074345..96075944,2	K562	blood:
2	chr10:96061164..96063335-chr10:96068490..96070582,2	K562	blood:
3	chr10:96066295..96067881-chr10:96069190..96071900,2	K562	blood:

Variant related genes	Relation type
ENSG00000273450	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10509670	0.82[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10509671	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882416	0.81[AMR][1000 genomes]
rs10882422	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10882424	1.00[MEX][hapmap]
rs10882435	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882436	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882437	0.93[MEX][hapmap]
rs11187837	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11187840	0.97[ASN][1000 genomes]
rs11187842	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11187845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11187847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11187850	0.83[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11187851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11187852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11187853	0.83[AMR][1000 genomes]
rs11187856	0.94[ASN][1000 genomes]
rs11187863	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11187864	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11187866	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11187869	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11187870	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11187877	0.87[ASN][1000 genomes]
rs11187882	0.85[ASN][1000 genomes]
rs11187883	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11187890	0.87[ASN][1000 genomes]
rs11187893	0.81[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11187894	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11187895	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11187897	0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11187899	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11187900	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11187901	0.93[MEX][hapmap]
rs11558740	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12217597	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12217792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12220091	0.97[ASN][1000 genomes]
rs12220125	0.87[AMR][1000 genomes]
rs12263737	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs12780491	0.81[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs12781451	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17109875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2274223	0.83[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3740359	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3740360	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3740365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3765524	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs3781265	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3781266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3818432	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs4394764	0.89[ASW][hapmap]
rs6583934	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6583935	0.85[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7081265	0.86[MEX][hapmap]
rs7084339	0.82[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7092226	0.86[MEX][hapmap]
rs7096678	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7096883	0.97[ASN][1000 genomes]
rs7099485	0.82[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7100430	0.93[MEX][hapmap]
rs7100626	0.97[ASN][1000 genomes]
rs752140	0.97[ASN][1000 genomes]
rs753724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7897678	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7897963	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7903902	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7908638	0.83[AMR][1000 genomes]
rs7914672	0.81[AMR][1000 genomes];0.85[EUR][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:1)

Disease	PMID	Source
Esophageal cancer and gastric cancer	20729852	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3781264	TCTN3	cis	parietal	SCAN
rs3781264	NOC3L	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96031800-96121000	Weak transcription	Stomach Mucosa	stomach
2	chr10:96036000-96081600	Weak transcription	Left Ventricle	heart
3	chr10:96043600-96121000	Weak transcription	Psoas Muscle	Psoas
4	chr10:96048800-96074800	Weak transcription	Placenta	Placenta
5	chr10:96049400-96081600	Weak transcription	Spleen	Spleen
6	chr10:96052800-96073600	Weak transcription	Ovary	ovary
7	chr10:96053000-96083200	Weak transcription	Fetal Kidney	kidney
8	chr10:96053200-96081600	Weak transcription	Brain Substantia Nigra	brain
9	chr10:96053400-96073000	Weak transcription	Fetal Lung	lung
10	chr10:96055200-96074600	Strong transcription	Fetal Muscle Leg	muscle
11	chr10:96059000-96074800	Weak transcription	Adipose Nuclei	Adipose
12	chr10:96059400-96083200	Weak transcription	Brain Anterior Caudate	brain
13	chr10:96059600-96081600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:96060000-96074800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:96063600-96076600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr10:96064200-96070600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr10:96064400-96073800	Strong transcription	Fetal Stomach	stomach
18	chr10:96064800-96071600	Strong transcription	Stomach Smooth Muscle	stomach
19	chr10:96064800-96072600	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr10:96066000-96074800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr10:96066200-96071000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr10:96066200-96071800	Strong transcription	HSMMtube	muscle
23	chr10:96066200-96074800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:96066400-96070400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:96066400-96075200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr10:96067200-96074800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:96067200-96075000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:96067400-96074800	Weak transcription	Pancreas	Pancrea
29	chr10:96067400-96081800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:96067400-96084400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:96068200-96071400	Strong transcription	Colonic Mucosa	Colon
32	chr10:96068600-96070600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:96068800-96070600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:96068800-96075600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:96069200-96071000	Strong transcription	Aorta	Aorta
36	chr10:96069200-96089800	Weak transcription	HUVEC	blood vessel
37	chr10:96069400-96071000	Genic enhancers	Fetal Intestine Large	intestine
38	chr10:96069400-96075600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:96069600-96072800	Weak transcription	A549	lung
40	chr10:96069600-96073600	Weak transcription	Gastric	stomach
41	chr10:96069600-96081600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:96069800-96071200	Genic enhancers	Fetal Intestine Small	intestine
43	chr10:96070000-96070400	Enhancers	Liver	Liver
44	chr10:96070000-96070400	Enhancers	Lung	lung
45	chr10:96070000-96070400	Flanking Active TSS	HepG2	liver
46	chr10:96070000-96071200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:96070200-96071000	Strong transcription	Fetal Brain Female	brain
48	chr10:96070200-96081800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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