Variant report

Variant	rs3181122
Chromosome Location	chr10:97607165-97607166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222986722..222989706-chr10:97605580..97607504,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTN3-1	chr10:97607149-97607242	ENSG00000226688.1
2	lnc-TCTN3-1	chr10:97607149-97607242	NONHSAT015766

Variant related genes	Relation type
ENSG00000228106	Chromatin interaction
ENSG00000154309	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10509686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509695	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10786239	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786247	0.82[CHB][hapmap]
rs10882649	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10882661	0.91[ASN][1000 genomes]
rs10882671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188417	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs11188444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188464	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188480	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188484	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11188489	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188501	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11188504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188506	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188509	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188516	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188531	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11593044	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11593761	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597321	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11598475	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12354848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12358481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12359343	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12359366	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12360382	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411569	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1340837	0.83[CEU][hapmap]
rs17382898	0.82[CHB][hapmap]
rs17461546	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17462179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17553401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891535	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1891536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935814	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861154	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176884	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3192654	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258314	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs4320886	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4344425	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4402217	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463786	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918970	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918972	0.87[AMR][1000 genomes];0.96[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	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074866	0.89[EUR][1000 genomes]
rs7089668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091088	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895056	0.82[CHB][hapmap]
rs7896876	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918339	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
rs3181122	ENTPD1	cis	multi-tissue	Pritchard
rs3181122	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs3181122	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 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	chr10:97601800-97607200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr10:97601800-97607400	Weak transcription	Brain Anterior Caudate	brain
14	chr10:97601800-97608800	Weak transcription	Colon Smooth Muscle	Colon
15	chr10:97601800-97609200	Strong transcription	GM12878-XiMat	blood
16	chr10:97601800-97624600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:97601800-97626000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr10:97601800-97626400	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:97601800-97627200	Weak transcription	Liver	Liver
20	chr10:97601800-97635400	Weak transcription	Brain Substantia Nigra	brain
21	chr10:97601800-97647800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:97602200-97611000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr10:97602400-97607800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:97602400-97610800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr10:97602400-97611000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr10:97602400-97655400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:97602600-97610800	Strong transcription	Primary B cells from cord blood	blood
28	chr10:97603000-97624800	Weak transcription	Fetal Intestine Small	intestine
29	chr10:97603200-97624800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr10:97603800-97620200	Weak transcription	Spleen	Spleen
31	chr10:97604400-97608000	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:97604400-97609800	Strong transcription	Aorta	Aorta
33	chr10:97605000-97607600	Weak transcription	Fetal Stomach	stomach
34	chr10:97605200-97607800	Weak transcription	Lung	lung
35	chr10:97605400-97620800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:97605600-97607200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:97605800-97607200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:97606800-97608200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:97606800-97610600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:97606800-97611000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr10:97607000-97610200	Strong transcription	Stomach Smooth Muscle	stomach

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