Variant report

Variant	rs56394995
Chromosome Location	chr8:52767763-52767764
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10086504	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10092494	0.97[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10097328	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10102568	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10504127	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10504132	0.88[ASN][1000 genomes]
rs12115132	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13281179	0.92[ASN][1000 genomes]
rs16916878	0.88[ASN][1000 genomes]
rs16916903	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16919843	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2020431	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28635761	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28652885	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873602	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4873609	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56128832	0.87[EUR][1000 genomes]
rs58408501	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58591247	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59344101	0.84[AMR][1000 genomes]
rs61196861	0.81[ASN][1000 genomes]
rs7008721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7010217	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7011046	0.88[ASN][1000 genomes]
rs73590413	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73592226	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7815751	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7843530	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs56394995	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52722000-52771400	Weak transcription	Gastric	stomach
2	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
5	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
6	chr8:52739800-52782600	Weak transcription	K562	blood
7	chr8:52743000-52771400	Weak transcription	HepG2	liver
8	chr8:52743400-52771400	Weak transcription	Esophagus	oesophagus
9	chr8:52744000-52768200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:52744000-52771200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr8:52744000-52771400	Weak transcription	Fetal Brain Female	brain
12	chr8:52744200-52770800	Weak transcription	Placenta	Placenta
13	chr8:52744400-52768600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:52744600-52769000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:52744600-52769200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr8:52745600-52768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr8:52745800-52769400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:52751000-52768000	Weak transcription	Fetal Muscle Leg	muscle
19	chr8:52751200-52771400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:52752400-52768000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr8:52752400-52771200	Weak transcription	Fetal Heart	heart
22	chr8:52754200-52771400	Weak transcription	NHLF	lung
23	chr8:52755000-52769000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:52757400-52769400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr8:52757400-52770600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr8:52757600-52768800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr8:52757600-52769200	Weak transcription	Osteobl	bone
28	chr8:52757600-52771400	Weak transcription	HSMM	muscle
29	chr8:52758400-52770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:52759000-52786200	Weak transcription	Lung	lung
31	chr8:52759200-52786200	Weak transcription	Spleen	Spleen
32	chr8:52760200-52769400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr8:52760600-52769400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:52762800-52768000	Weak transcription	Dnd41	blood
35	chr8:52762800-52768800	Weak transcription	A549	lung
36	chr8:52762800-52769000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr8:52762800-52769600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:52763600-52769000	Weak transcription	Primary B cells from cord blood	blood
39	chr8:52763800-52771400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr8:52763800-52772600	Weak transcription	Fetal Kidney	kidney
41	chr8:52763800-52781800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr8:52764000-52768800	Weak transcription	Primary T cells from cord blood	blood
43	chr8:52764000-52768800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr8:52764000-52768800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr8:52764000-52769000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr8:52764000-52769800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr8:52764000-52770400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr8:52764000-52771000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr8:52764000-52774600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr8:52764000-52779400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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