Variant report

Variant	rs4075311
Chromosome Location	chr10:97574655-97574656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10159941	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs10509687	0.93[JPT][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap]
rs10736093	0.94[CHB][hapmap];0.83[TSI][hapmap]
rs10748635	0.90[JPT][hapmap];0.95[YRI][hapmap]
rs10748637	0.93[JPT][hapmap];0.96[YRI][hapmap]
rs10748642	0.94[CHB][hapmap]
rs10748643	0.94[CHB][hapmap]
rs10748648	1.00[CHB][hapmap]
rs10786230	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs10786235	0.82[CHD][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs10786236	0.94[CHB][hapmap]
rs10882651	0.83[CHB][hapmap]
rs10882652	0.83[CHB][hapmap]
rs10882653	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs10882656	0.94[CHB][hapmap]
rs10882657	0.94[CHB][hapmap]
rs10882660	0.94[CHB][hapmap]
rs10882670	0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10882673	1.00[CHB][hapmap]
rs10882675	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs10882676	1.00[CHB][hapmap]
rs11188459	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11188470	0.81[AFR][1000 genomes]
rs11188482	0.88[AFR][1000 genomes]
rs11188485	0.86[JPT][hapmap]
rs11188486	0.94[CHB][hapmap]
rs11188488	0.85[JPT][hapmap]
rs11188497	0.93[CHB][hapmap]
rs11188513	0.94[CHB][hapmap]
rs11528098	0.87[AFR][1000 genomes]
rs12240959	0.89[AFR][1000 genomes]
rs12244559	0.88[CHB][hapmap]
rs12262943	0.86[JPT][hapmap]
rs1340837	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1342790	0.94[CHB][hapmap]
rs1418709	0.94[CHB][hapmap]
rs1573112	0.87[CHB][hapmap];0.83[TSI][hapmap]
rs17111041	0.86[JPT][hapmap]
rs1933165	0.94[CHB][hapmap]
rs1933166	0.82[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs1953710	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2051052	0.94[CHB][hapmap]
rs2096219	0.97[ASN][1000 genomes]
rs2153913	0.94[CHB][hapmap]
rs2153914	0.94[CHB][hapmap]
rs2185818	0.94[CHB][hapmap]
rs2225893	0.93[JPT][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs2226163	0.93[CHB][hapmap]
rs2275759	0.94[CHB][hapmap]
rs2297788	0.83[CHB][hapmap]
rs2861147	0.94[CHB][hapmap]
rs2861148	0.94[CHB][hapmap]
rs3176881	0.94[CHB][hapmap]
rs3176883	0.82[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap]
rs3176891	0.94[CHB][hapmap]
rs3181124	0.94[CHB][hapmap];0.83[TSI][hapmap]
rs3181129	0.88[CHB][hapmap]
rs3181131	0.94[CHB][hapmap]
rs3793748	0.92[JPT][hapmap];0.92[YRI][hapmap]
rs3814159	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs3929900	0.94[CHB][hapmap]
rs3934409	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs4074424	0.94[CHB][hapmap]
rs4075310	0.94[CHB][hapmap]
rs4396219	0.94[CHB][hapmap]
rs4409759	0.89[AFR][1000 genomes]
rs4431963	0.94[CHB][hapmap]
rs4457685	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs4551688	0.94[CHB][hapmap]
rs4582902	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs4614366	0.88[CHB][hapmap]
rs4918962	0.94[CHB][hapmap]
rs4918964	0.84[JPT][hapmap]
rs5014871	0.94[CHB][hapmap]
rs60227189	0.85[AFR][1000 genomes]
rs6584022	0.94[CHB][hapmap]
rs6584023	0.94[CHB][hapmap]
rs6584026	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs6584027	0.94[CHB][hapmap];0.82[TSI][hapmap]
rs6584028	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6584031	0.89[AFR][1000 genomes]
rs6584033	0.82[CHD][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7067762	0.93[CHB][hapmap]
rs7069234	0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7071836	0.94[CHB][hapmap]
rs7073723	0.82[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs7074403	0.94[CHB][hapmap]
rs7077566	0.94[CHB][hapmap]
rs7081414	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7086986	0.94[CHB][hapmap]
rs7088584	0.94[CHB][hapmap]
rs7095587	0.94[CHB][hapmap]
rs7096317	0.94[CHB][hapmap]
rs7098750	0.93[JPT][hapmap]
rs7894648	0.83[CHB][hapmap]
rs7901116	0.86[AFR][1000 genomes]
rs7905653	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7915345	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7920801	0.83[CHB][hapmap]
rs7920850	0.93[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap]

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	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4075311	ENTPD1	cis	lymphoblastoid	seeQTL
rs4075311	TCTN3	Cis_1M	lymphoblastoid	RTeQTL
rs4075311	ALDH18A1	cis	cerebellum	SCAN
rs4075311	ENTPD1	cis	Lymphoblastoid	GTEx
rs4075311	ENTPD1	cis	multi-tissue	Pritchard
rs4075311	TCTN3	cis	lymphoblastoid	seeQTL
rs4075311	ALDH18A1	cis	parietal	SCAN
rs4075311	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs4075311	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97553000-97576200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:97570400-97577600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:97572000-97575200	Enhancers	HepG2	liver
4	chr10:97573000-97575400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr10:97573000-97575400	Enhancers	Brain Anterior Caudate	brain
6	chr10:97573000-97575800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:97573000-97575800	Enhancers	Brain Hippocampus Middle	brain
8	chr10:97573200-97574800	Enhancers	HMEC	breast
9	chr10:97573200-97574800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr10:97573200-97575000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr10:97573200-97575200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr10:97573200-97575200	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr10:97573200-97575800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:97573200-97575800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr10:97573200-97580000	Enhancers	HUVEC	blood vessel
16	chr10:97573400-97575400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr10:97573400-97575800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr10:97573600-97575400	Enhancers	Brain Substantia Nigra	brain
19	chr10:97573800-97574800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:97573800-97584400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:97574000-97574800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:97574000-97575000	Weak transcription	Esophagus	oesophagus
23	chr10:97574000-97575200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:97574000-97575400	Weak transcription	Aorta	Aorta
25	chr10:97574000-97575600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr10:97574200-97575000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr10:97574200-97575200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr10:97574200-97575200	Weak transcription	Adipose Nuclei	Adipose
29	chr10:97574200-97575200	Weak transcription	Brain Angular Gyrus	brain
30	chr10:97574200-97575200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:97574200-97575400	Genic enhancers	GM12878-XiMat	blood
32	chr10:97574200-97575600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:97574200-97583000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:97574400-97575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr10:97574400-97575400	Weak transcription	Lung	lung
36	chr10:97574400-97575600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr10:97574400-97575600	Weak transcription	Placenta	Placenta
38	chr10:97574400-97575600	Weak transcription	Left Ventricle	heart
39	chr10:97574400-97576800	Weak transcription	Fetal Stomach	stomach
40	chr10:97574400-97578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:97574400-97578200	Weak transcription	Right Ventricle	heart
42	chr10:97574400-97580800	Weak transcription	Small Intestine	intestine
43	chr10:97574400-97581000	Weak transcription	Spleen	Spleen
44	chr10:97574400-97581400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:97574600-97575000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr10:97574600-97575800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:97574600-97576400	Weak transcription	Primary B cells from cord blood	blood
48	chr10:97574600-97578200	Weak transcription	NHLF	lung
49	chr10:97574600-97578400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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