Variant report

Variant	rs1078888
Chromosome Location	chr8:52741761-52741762
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10086351	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10086504	0.87[JPT][hapmap]
rs10095651	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10095739	0.82[EUR][1000 genomes]
rs10096943	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10097328	0.87[JPT][hapmap]
rs10110304	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1022315	0.82[EUR][1000 genomes]
rs1022316	0.82[EUR][1000 genomes]
rs1022317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10435632	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10504128	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10504132	0.86[JPT][hapmap]
rs1059041	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1073371	0.80[EUR][1000 genomes]
rs10958298	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10958299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10958302	0.82[EUR][1000 genomes]
rs10958303	0.82[EUR][1000 genomes]
rs11775601	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11777316	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11777386	0.82[AFR][1000 genomes]
rs11777885	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11782696	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11782730	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11784921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11786126	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12334986	0.80[EUR][1000 genomes]
rs12546934	0.80[EUR][1000 genomes]
rs12675156	0.82[EUR][1000 genomes]
rs12675404	0.82[EUR][1000 genomes]
rs12676361	0.82[EUR][1000 genomes]
rs12677434	0.81[AMR][1000 genomes]
rs12678479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12680771	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12680958	0.82[EUR][1000 genomes]
rs12681673	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12681867	0.82[EUR][1000 genomes]
rs12682564	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13250860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13252580	0.82[EUR][1000 genomes]
rs13256408	0.82[EUR][1000 genomes]
rs13257067	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13257291	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13257720	0.80[EUR][1000 genomes]
rs13258269	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13261243	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13264242	0.81[EUR][1000 genomes]
rs13265029	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13266326	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13267846	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13268128	0.80[EUR][1000 genomes]
rs13268907	0.82[EUR][1000 genomes]
rs13268938	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13269881	0.82[EUR][1000 genomes]
rs13271572	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13272178	0.82[EUR][1000 genomes]
rs13272467	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13274160	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13275045	0.80[EUR][1000 genomes]
rs13275235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13280391	0.80[EUR][1000 genomes]
rs13280413	0.82[EUR][1000 genomes]
rs13280471	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13281179	0.87[JPT][hapmap]
rs1517304	0.82[EUR][1000 genomes]
rs1517305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs16916810	0.80[EUR][1000 genomes]
rs16916878	0.83[JPT][hapmap]
rs1914370	0.82[EUR][1000 genomes]
rs2395857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs3763547	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3824266	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4259408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4291261	0.80[EUR][1000 genomes]
rs4294173	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4313145	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4324911	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4330683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4352840	0.80[EUR][1000 genomes]
rs4361755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4395889	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4401852	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4442135	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4487755	0.80[EUR][1000 genomes]
rs4570148	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4584139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4587320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4596648	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4612332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4618684	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4634632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4642637	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4873206	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4873207	0.82[EUR][1000 genomes]
rs4873604	0.80[EUR][1000 genomes]
rs4873606	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4873608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4873610	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4873613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4873616	0.82[EUR][1000 genomes]
rs5002416	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5003717	0.80[EUR][1000 genomes]
rs6983163	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6986984	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6990552	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6999031	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7000493	0.80[AMR][1000 genomes]
rs7008057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7010217	0.86[JPT][hapmap]
rs7011046	0.87[JPT][hapmap];0.83[YRI][hapmap]
rs7012360	0.80[EUR][1000 genomes]
rs7013587	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7014075	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7017450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7460311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7463120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7464192	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7465225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs753539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs756484	0.80[EUR][1000 genomes]
rs7818832	0.80[EUR][1000 genomes]
rs7829408	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7833777	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs882492	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs884580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs925761	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs925763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9298463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9298464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9298465	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9298466	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9298467	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs950687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9643466	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9643790	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9643791	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9643792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9643793	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][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
rs1078888	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52717600-52741800	Weak transcription	Aorta	Aorta
2	chr8:52719400-52741800	Weak transcription	Esophagus	oesophagus
3	chr8:52722000-52771400	Weak transcription	Gastric	stomach
4	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
5	chr8:52722400-52741800	Weak transcription	Right Ventricle	heart
6	chr8:52722800-52741800	Weak transcription	HSMMtube	muscle
7	chr8:52726000-52741800	Weak transcription	Brain Substantia Nigra	brain
8	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
9	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
13	chr8:52731800-52741800	Weak transcription	Psoas Muscle	Psoas
14	chr8:52731800-52745600	Weak transcription	NHEK	skin
15	chr8:52732200-52743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr8:52732200-52746000	Weak transcription	Fetal Brain Male	brain
17	chr8:52732200-52746400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr8:52732800-52753600	Weak transcription	Osteobl	bone
19	chr8:52733200-52742600	Weak transcription	HepG2	liver
20	chr8:52733200-52758800	Weak transcription	Small Intestine	intestine
21	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr8:52733400-52741800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:52733400-52757200	Weak transcription	Colonic Mucosa	Colon
25	chr8:52733600-52745200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr8:52733800-52742000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
28	chr8:52734000-52742600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr8:52734400-52745200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:52735400-52741800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:52735400-52741800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:52735400-52741800	Weak transcription	Lung	lung
34	chr8:52735400-52744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr8:52735400-52753400	Weak transcription	HUVEC	blood vessel
36	chr8:52735600-52741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr8:52735600-52741800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr8:52735600-52753800	Weak transcription	HSMM	muscle
39	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
41	chr8:52735800-52741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr8:52735800-52741800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr8:52735800-52742000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:52735800-52742800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr8:52735800-52753600	Weak transcription	Hela-S3	cervix
46	chr8:52735800-52763400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr8:52736000-52741800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr8:52736000-52741800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr8:52736000-52741800	Weak transcription	Adipose Nuclei	Adipose
50	chr8:52736000-52741800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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