Variant report

Variant	rs3192654
Chromosome Location	chr10:97632808-97632809
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10509686	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786239	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786247	0.81[YRI][hapmap]
rs10882661	0.91[ASN][1000 genomes]
rs10882671	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188444	0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs11188455	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188464	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188480	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188484	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11188489	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188501	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188504	0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188506	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188509	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188516	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593044	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11593761	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597321	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11598475	0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354848	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357173	0.91[YRI][hapmap]
rs12358481	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12359343	0.80[AFR][1000 genomes]
rs12359366	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12360382	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461546	0.89[YRI][hapmap]
rs17462179	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17553401	0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891535	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891536	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935814	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935815	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861151	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861153	0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861154	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176884	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176895	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181122	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320886	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4402217	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463786	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512761	0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568937	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918966	0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918970	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918972	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801606	0.83[ASN][1000 genomes]
rs61869573	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61869591	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074866	0.92[EUR][1000 genomes]
rs7089668	0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091088	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896876	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918339	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3192654	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs3192654	ENTPD1	cis	multi-tissue	Pritchard
rs3192654	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97601600-97635600	Weak transcription	Fetal Brain Male	brain
2	chr10:97601800-97635400	Weak transcription	Brain Substantia Nigra	brain
3	chr10:97601800-97647800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:97602400-97655400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:97615400-97634400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr10:97615800-97633800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr10:97615800-97634400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:97619400-97633000	Weak transcription	Fetal Brain Female	brain
9	chr10:97619600-97655000	Weak transcription	HUVEC	blood vessel
10	chr10:97619800-97633400	Weak transcription	A549	lung
11	chr10:97620800-97633000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:97621000-97640600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr10:97621000-97666800	Weak transcription	Gastric	stomach
14	chr10:97622800-97666600	Weak transcription	Thymus	Thymus
15	chr10:97623800-97666600	Weak transcription	Right Ventricle	heart
16	chr10:97624800-97635000	Weak transcription	Small Intestine	intestine
17	chr10:97625000-97633000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:97625000-97633200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:97625000-97634200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:97625200-97634200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr10:97625200-97635800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:97625200-97636800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:97625200-97655200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:97625400-97648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:97625400-97649200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:97625400-97666400	Weak transcription	Osteobl	bone
27	chr10:97625600-97633400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr10:97626000-97633000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:97626000-97633200	Weak transcription	Brain Germinal Matrix	brain
30	chr10:97626000-97637000	Weak transcription	HSMMtube	muscle
31	chr10:97626200-97633000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:97626200-97638000	Weak transcription	Fetal Kidney	kidney
33	chr10:97626400-97666400	Weak transcription	Pancreas	Pancrea
34	chr10:97626800-97634000	Weak transcription	Fetal Intestine Small	intestine
35	chr10:97626800-97639600	Weak transcription	HepG2	liver
36	chr10:97626800-97654200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:97627600-97633600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr10:97628000-97635600	Weak transcription	HMEC	breast
39	chr10:97628000-97666800	Weak transcription	Esophagus	oesophagus
40	chr10:97628200-97647800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:97628200-97655600	Weak transcription	Brain Anterior Caudate	brain
42	chr10:97628400-97636000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr10:97628400-97657600	Weak transcription	Hela-S3	cervix
44	chr10:97628600-97634200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:97628600-97634200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr10:97629000-97633000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:97629200-97633000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr10:97629200-97633200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr10:97629200-97647800	Weak transcription	NHEK	skin
50	chr10:97629200-97655200	Weak transcription	NH-A	brain

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