Variant report

Variant	rs12359343
Chromosome Location	chr10:97660572-97660573
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97657059..97661839-chr10:97664974..97668888,4	K562	blood:
2	chr10:97654990..97656934-chr10:97659320..97661534,2	K562	blood:

Variant related genes	Relation type
ENSG00000226688	Chromatin interaction
ENSG00000173088	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10509686	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10509695	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs10786239	0.82[AFR][1000 genomes]
rs10786247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882654	0.85[CHB][hapmap]
rs10882671	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10882698	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10882718	1.00[JPT][hapmap]
rs11188444	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11188455	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11188484	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11188504	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs11188516	0.80[AFR][1000 genomes]
rs11188530	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs11188531	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs11188575	1.00[JPT][hapmap]
rs11188596	1.00[JPT][hapmap]
rs11598475	1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12354848	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12358481	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12411569	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12415750	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17382898	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17462179	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs17553401	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs1891536	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs1935814	0.82[AFR][1000 genomes]
rs1935815	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs2861151	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs2861153	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs3176895	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs3181122	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3192654	0.80[AFR][1000 genomes]
rs3961944	1.00[JPT][hapmap]
rs4325250	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs4344425	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap]
rs4391761	0.94[EUR][1000 genomes]
rs4512761	0.86[ASW][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes]
rs4918966	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap]
rs4918976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56365500	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57294882	0.80[EUR][1000 genomes]
rs61559520	0.80[EUR][1000 genomes]
rs61871074	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7089668	0.86[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap]
rs7091088	0.85[AFR][1000 genomes]
rs7895056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7896876	0.85[AFR][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12359343	ENTPD1	cis	multi-tissue	Pritchard
rs12359343	ENTPD1	cis	lymphoblastoid	seeQTL
rs12359343	ALDH18A1	cis	cerebellum	SCAN
rs12359343	PDLIM1	cis	brain	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97621000-97666800	Weak transcription	Gastric	stomach
2	chr10:97622800-97666600	Weak transcription	Thymus	Thymus
3	chr10:97623800-97666600	Weak transcription	Right Ventricle	heart
4	chr10:97625400-97666400	Weak transcription	Osteobl	bone
5	chr10:97626400-97666400	Weak transcription	Pancreas	Pancrea
6	chr10:97628000-97666800	Weak transcription	Esophagus	oesophagus
7	chr10:97629200-97663000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:97631200-97663000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:97632200-97667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:97633400-97666600	Weak transcription	Brain Angular Gyrus	brain
11	chr10:97633800-97666600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:97633800-97666600	Weak transcription	Brain Hippocampus Middle	brain
13	chr10:97634000-97663200	Weak transcription	Spleen	Spleen
14	chr10:97634400-97666800	Weak transcription	Lung	lung
15	chr10:97634600-97666400	Weak transcription	Brain Germinal Matrix	brain
16	chr10:97634600-97666800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:97634800-97667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:97635800-97666600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:97636400-97662600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr10:97636400-97666400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr10:97636800-97666400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr10:97638600-97666600	Weak transcription	Colonic Mucosa	Colon
23	chr10:97641200-97662800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:97643200-97666600	Weak transcription	Fetal Heart	heart
25	chr10:97644600-97661400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr10:97646600-97666400	Weak transcription	HSMM	muscle
27	chr10:97648000-97662600	Weak transcription	K562	blood
28	chr10:97648000-97666400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr10:97649400-97662400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr10:97649400-97666600	Weak transcription	Fetal Intestine Large	intestine
31	chr10:97650000-97666600	Weak transcription	Fetal Intestine Small	intestine
32	chr10:97650200-97662600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:97651800-97666400	Weak transcription	A549	lung
34	chr10:97652200-97666400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr10:97652800-97662400	Weak transcription	Brain Substantia Nigra	brain
36	chr10:97652800-97662400	Weak transcription	Dnd41	blood
37	chr10:97653800-97666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:97654000-97664800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:97654000-97665000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:97654200-97660600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:97654400-97664800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr10:97654400-97665000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:97654600-97663600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:97655000-97664400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:97655200-97660600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:97655200-97660600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr10:97655200-97666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:97655800-97666600	Weak transcription	HSMMtube	muscle
49	chr10:97656000-97661800	Weak transcription	Placenta	Placenta
50	chr10:97656200-97662600	Weak transcription	NH-A	brain

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