Variant report

Variant	rs3176884
Chromosome Location	chr10:97604651-97604652
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10509686	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786239	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882661	0.91[ASN][1000 genomes]
rs10882671	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188444	0.83[ASN][1000 genomes]
rs11188455	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188464	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188480	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188484	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11188489	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188501	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188506	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188509	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188516	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11593044	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11593761	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597321	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11598475	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354848	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358481	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12359366	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12360382	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17462179	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17553401	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891535	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891536	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935814	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935815	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861151	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861153	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861154	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176895	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3181122	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3192654	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320886	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4402217	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463786	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512761	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568937	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4918966	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918970	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918972	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801606	0.83[ASN][1000 genomes]
rs61869573	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61869591	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074866	0.90[EUR][1000 genomes]
rs7089668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091088	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7896876	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918339	0.86[AFR][1000 genomes];0.80[AMR][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
rs3176884	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs3176884	ENTPD1	cis	multi-tissue	Pritchard
rs3176884	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97592000-97607200	Weak transcription	Left Ventricle	heart
2	chr10:97592600-97632800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:97597200-97627200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:97597400-97624600	Weak transcription	Placenta	Placenta
5	chr10:97597400-97627400	Weak transcription	Brain Angular Gyrus	brain
6	chr10:97597600-97609600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr10:97597600-97620600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:97600600-97628600	Weak transcription	Colonic Mucosa	Colon
9	chr10:97601200-97624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:97601600-97624400	Weak transcription	Fetal Intestine Large	intestine
11	chr10:97601600-97635600	Weak transcription	Fetal Brain Male	brain
12	chr10:97601800-97605200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr10:97601800-97607200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:97601800-97607400	Weak transcription	Brain Anterior Caudate	brain
15	chr10:97601800-97608800	Weak transcription	Colon Smooth Muscle	Colon
16	chr10:97601800-97609200	Strong transcription	GM12878-XiMat	blood
17	chr10:97601800-97624600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr10:97601800-97626000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:97601800-97626400	Weak transcription	Brain Hippocampus Middle	brain
20	chr10:97601800-97627200	Weak transcription	Liver	Liver
21	chr10:97601800-97635400	Weak transcription	Brain Substantia Nigra	brain
22	chr10:97601800-97647800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:97602200-97605200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr10:97602200-97611000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr10:97602400-97605200	Weak transcription	Fetal Kidney	kidney
26	chr10:97602400-97606000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr10:97602400-97607800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:97602400-97610800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr10:97602400-97611000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr10:97602400-97655400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:97602600-97605600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr10:97602600-97610800	Strong transcription	Primary B cells from cord blood	blood
33	chr10:97603000-97624800	Weak transcription	Fetal Intestine Small	intestine
34	chr10:97603200-97624800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:97603400-97605800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr10:97603800-97620200	Weak transcription	Spleen	Spleen
37	chr10:97604000-97605800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:97604200-97605400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:97604200-97605400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr10:97604400-97604800	Weak transcription	Fetal Stomach	stomach
41	chr10:97604400-97608000	Weak transcription	Fetal Muscle Leg	muscle
42	chr10:97604400-97609800	Strong transcription	Aorta	Aorta
43	chr10:97604600-97605000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr10:97604600-97605200	Strong transcription	Lung	lung

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