Variant report

Variant	rs13281179
Chromosome Location	chr8:52746752-52746753
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10086504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10092494	0.91[ASN][1000 genomes]
rs10096943	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs10097328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10102568	0.94[ASN][1000 genomes]
rs10104368	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10110304	0.82[JPT][hapmap]
rs1022317	0.86[JPT][hapmap]
rs10435632	0.87[AFR][1000 genomes]
rs10504127	0.89[ASN][1000 genomes]
rs10504128	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs10504132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1059041	0.86[JPT][hapmap]
rs1078888	0.87[JPT][hapmap]
rs10958299	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs10958308	0.80[CHB][hapmap]
rs11775601	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs11777316	0.87[AFR][1000 genomes]
rs11777386	0.83[AFR][1000 genomes]
rs11777885	0.94[JPT][hapmap];0.87[AFR][1000 genomes]
rs11782730	0.87[AFR][1000 genomes]
rs11784921	0.88[JPT][hapmap];0.87[AFR][1000 genomes]
rs12115132	0.92[ASN][1000 genomes]
rs12678479	0.86[JPT][hapmap]
rs13250860	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs13257067	0.87[JPT][hapmap];0.83[AFR][1000 genomes]
rs13257291	0.87[JPT][hapmap]
rs13261243	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs13265029	0.83[AFR][1000 genomes]
rs13266326	0.87[AFR][1000 genomes]
rs13268938	0.87[AFR][1000 genomes]
rs13272467	0.83[AFR][1000 genomes]
rs13275235	0.87[JPT][hapmap]
rs1517305	0.87[JPT][hapmap]
rs16916800	0.85[ASN][1000 genomes]
rs16916878	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16916903	0.97[ASN][1000 genomes]
rs16916974	0.80[ASN][1000 genomes]
rs16919843	0.86[ASN][1000 genomes]
rs2020431	0.97[ASN][1000 genomes]
rs2395857	0.86[JPT][hapmap]
rs28635761	0.82[ASN][1000 genomes]
rs28652885	0.82[ASN][1000 genomes]
rs3763547	0.81[JPT][hapmap]
rs3824266	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs4259408	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs4294173	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs4313145	0.87[AFR][1000 genomes]
rs4324911	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs4330683	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs4361755	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs4570148	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs4584139	0.87[JPT][hapmap];0.83[AFR][1000 genomes]
rs4587320	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs4596648	0.87[JPT][hapmap]
rs4612332	0.87[JPT][hapmap]
rs4618684	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs4634632	0.87[JPT][hapmap]
rs4873206	0.87[AFR][1000 genomes]
rs4873602	0.83[ASN][1000 genomes]
rs4873608	0.87[JPT][hapmap]
rs4873609	0.95[ASN][1000 genomes]
rs4873610	0.83[AFR][1000 genomes]
rs4873613	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs5002416	0.82[JPT][hapmap];0.87[AFR][1000 genomes]
rs56394995	0.92[ASN][1000 genomes]
rs58408501	0.83[ASN][1000 genomes]
rs58591247	0.88[ASN][1000 genomes]
rs61196861	0.86[ASN][1000 genomes]
rs6983163	0.87[AFR][1000 genomes]
rs6986984	0.87[AFR][1000 genomes]
rs6990552	0.87[AFR][1000 genomes]
rs7008057	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs7008721	0.82[ASN][1000 genomes]
rs7010217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7011046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7013587	0.87[JPT][hapmap]
rs7014075	0.87[JPT][hapmap]
rs7017450	0.87[JPT][hapmap]
rs73590413	0.82[ASN][1000 genomes]
rs73592226	0.97[ASN][1000 genomes]
rs7460311	0.87[JPT][hapmap]
rs7463120	0.87[JPT][hapmap];0.85[AFR][1000 genomes]
rs7464192	0.87[JPT][hapmap]
rs7465225	0.86[JPT][hapmap]
rs753540	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs7815751	0.89[ASN][1000 genomes]
rs7829408	0.87[JPT][hapmap]
rs7833777	0.87[AFR][1000 genomes]
rs7843530	0.92[ASN][1000 genomes]
rs882492	0.87[JPT][hapmap]
rs884580	0.87[JPT][hapmap]
rs925763	0.87[JPT][hapmap]
rs9298463	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs9298464	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs9298465	0.87[AFR][1000 genomes]
rs9298466	0.87[JPT][hapmap]
rs9298467	0.81[JPT][hapmap]
rs950687	0.87[JPT][hapmap]
rs9643466	0.86[JPT][hapmap];0.87[AFR][1000 genomes]
rs9643790	0.87[AFR][1000 genomes]
rs9643791	0.87[AFR][1000 genomes]
rs9643792	0.87[JPT][hapmap];0.87[AFR][1000 genomes]
rs9643793	0.87[JPT][hapmap];0.87[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	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13281179	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52722000-52771400	Weak transcription	Gastric	stomach
2	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
3	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
4	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
8	chr8:52732800-52753600	Weak transcription	Osteobl	bone
9	chr8:52733200-52758800	Weak transcription	Small Intestine	intestine
10	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:52733400-52757200	Weak transcription	Colonic Mucosa	Colon
13	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
14	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr8:52735400-52753400	Weak transcription	HUVEC	blood vessel
16	chr8:52735600-52753800	Weak transcription	HSMM	muscle
17	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
19	chr8:52735800-52753600	Weak transcription	Hela-S3	cervix
20	chr8:52735800-52763400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr8:52736000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:52736000-52753600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:52736200-52753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:52737200-52760400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:52737600-52753600	Weak transcription	NH-A	brain
26	chr8:52738200-52752000	Weak transcription	Right Atrium	heart
27	chr8:52738200-52753600	Weak transcription	A549	lung
28	chr8:52739800-52747000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:52739800-52765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:52739800-52782600	Weak transcription	K562	blood
31	chr8:52740200-52753400	Weak transcription	HMEC	breast
32	chr8:52740600-52753600	Weak transcription	Stomach Mucosa	stomach
33	chr8:52741000-52746800	Strong transcription	Fetal Thymus	thymus
34	chr8:52741200-52748800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr8:52741600-52746800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr8:52741600-52753600	Weak transcription	NHLF	lung
37	chr8:52742000-52765400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr8:52742400-52746800	Weak transcription	Fetal Heart	heart
39	chr8:52742600-52763400	Weak transcription	Brain Substantia Nigra	brain
40	chr8:52743000-52757600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr8:52743000-52771400	Weak transcription	HepG2	liver
42	chr8:52743200-52748600	Weak transcription	Psoas Muscle	Psoas
43	chr8:52743200-52765400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr8:52743400-52758800	Weak transcription	Brain Anterior Caudate	brain
45	chr8:52743400-52763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr8:52743400-52766200	Weak transcription	HSMMtube	muscle
47	chr8:52743400-52771400	Weak transcription	Esophagus	oesophagus
48	chr8:52743600-52757200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:52743600-52758800	Weak transcription	Spleen	Spleen
50	chr8:52743800-52750400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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