Variant report

Variant	rs3181123
Chromosome Location	chr10:97607075-97607076
allele	A/G
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:

Variant related genes	Relation type
ENSG00000154309	Chromatin interaction
ENSG00000228106	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10159941	0.92[CHB][hapmap]
rs10736093	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10736094	0.80[ASN][1000 genomes]
rs10748635	0.92[CHB][hapmap]
rs10748637	0.92[CHB][hapmap]
rs10748638	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10748642	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10748643	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10748648	0.88[JPT][hapmap]
rs10748649	0.84[ASN][1000 genomes]
rs10786230	0.92[CHB][hapmap]
rs10786233	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10786235	0.92[CHB][hapmap]
rs10786236	0.94[JPT][hapmap]
rs10882646	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10882647	0.85[JPT][hapmap]
rs10882651	0.90[JPT][hapmap]
rs10882652	0.90[JPT][hapmap]
rs10882653	0.92[CHB][hapmap]
rs10882656	0.94[JPT][hapmap]
rs10882657	0.94[JPT][hapmap]
rs10882660	0.94[JPT][hapmap]
rs10882664	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882665	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882668	0.80[ASN][1000 genomes]
rs10882670	0.92[CHB][hapmap]
rs10882673	0.83[JPT][hapmap]
rs10882675	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs10882676	0.83[JPT][hapmap]
rs11188414	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11188459	0.92[CHB][hapmap]
rs11188485	0.92[CHB][hapmap]
rs11188486	0.94[JPT][hapmap]
rs11188488	0.92[CHB][hapmap]
rs11188497	0.93[JPT][hapmap]
rs11188513	0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12244559	0.90[JPT][hapmap]
rs12262943	0.92[CHB][hapmap]
rs1342790	0.94[JPT][hapmap]
rs1342791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1418709	0.94[JPT][hapmap]
rs1573112	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs1891534	0.80[ASN][1000 genomes]
rs1933165	0.94[JPT][hapmap]
rs1933166	0.92[CHB][hapmap]
rs1933169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1953710	0.92[CHB][hapmap]
rs2051052	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2153913	0.94[JPT][hapmap]
rs2153914	0.82[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2185818	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2211002	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2225893	0.85[CHB][hapmap]
rs2226163	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2275759	0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2297788	0.90[JPT][hapmap]
rs2861147	0.94[JPT][hapmap]
rs2861148	0.94[JPT][hapmap]
rs2861149	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2901873	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176881	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs3176883	0.92[CHB][hapmap]
rs3176885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176891	0.94[JPT][hapmap]
rs3181124	0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs3181129	0.89[JPT][hapmap]
rs3181131	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3814159	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3929900	0.94[JPT][hapmap]
rs3934409	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3949478	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap]
rs4074424	0.94[JPT][hapmap]
rs4075310	0.94[JPT][hapmap]
rs4290159	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4396219	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4431963	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4457685	0.92[CHB][hapmap]
rs4501930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[EUR][1000 genomes]
rs4551688	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4582902	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4614366	0.90[JPT][hapmap]
rs4918962	0.94[JPT][hapmap]
rs4918964	1.00[CHB][hapmap]
rs5014871	0.94[JPT][hapmap]
rs57126367	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6584022	0.94[JPT][hapmap]
rs6584023	0.94[JPT][hapmap]
rs6584026	0.92[CHB][hapmap]
rs6584027	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6584028	0.92[CHB][hapmap]
rs6584033	0.92[CHB][hapmap]
rs7067762	0.94[JPT][hapmap]
rs7069234	0.92[CHB][hapmap]
rs7071836	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7072572	0.85[EUR][1000 genomes]
rs7073723	0.92[CHB][hapmap]
rs7074403	0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7077566	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7081414	0.92[CHB][hapmap]
rs7086986	0.94[JPT][hapmap]
rs7088584	0.85[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs7088961	0.80[ASN][1000 genomes]
rs7095587	0.94[JPT][hapmap]
rs7096317	0.89[JPT][hapmap]
rs7098750	0.92[CHB][hapmap]
rs7893677	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7894648	0.90[JPT][hapmap]
rs7902190	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7905653	0.92[CHB][hapmap]
rs7915345	0.92[CHB][hapmap]
rs7919196	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7920801	0.87[JPT][hapmap]
rs7920850	0.92[CHB][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3181123	ALDH18A1	cis	cerebellum	SCAN
rs3181123	ENTPD1	cis	Lymphoblastoid	GTEx
rs3181123	C10orf12	cis	cerebellum	SCAN
rs3181123	ENTPD1	cis	lymphoblastoid	seeQTL
rs3181123	TCTN3	cis	lymphoblastoid	seeQTL

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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