Variant report

Variant	rs10102568
Chromosome Location	chr8:52789977-52789978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:52789836..52792146-chr8:52797472..52799368,2	K562	blood:
2	chr8:52787298..52790273-chr8:52793803..52795714,2	K562	blood:
3	chr8:52788190..52790845-chr8:52803615..52805277,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10086504	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10092494	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10097328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10504127	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10504132	1.00[ASN][1000 genomes]
rs12115132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13281179	0.94[ASN][1000 genomes]
rs16916800	0.82[ASN][1000 genomes]
rs16916878	0.91[ASN][1000 genomes]
rs16916903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916974	0.86[ASN][1000 genomes]
rs16916979	0.84[ASN][1000 genomes]
rs16919843	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2020431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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]
rs28754887	0.82[ASN][1000 genomes]
rs4873602	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4873609	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56128832	0.87[EUR][1000 genomes]
rs56394995	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58408501	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58591247	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59344101	0.84[AMR][1000 genomes]
rs61196861	0.92[ASN][1000 genomes]
rs7008721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7010217	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7011046	1.00[ASN][1000 genomes]
rs73590413	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73592226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7815751	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7843530	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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
rs10102568	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52764000-52793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr8:52767400-52796600	Weak transcription	Fetal Brain Male	brain
3	chr8:52769800-52793600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:52771000-52797800	Weak transcription	Fetal Stomach	stomach
5	chr8:52771800-52797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:52771800-52810800	Weak transcription	Esophagus	oesophagus
7	chr8:52772200-52807600	Weak transcription	HSMMtube	muscle
8	chr8:52772400-52793200	Weak transcription	Fetal Heart	heart
9	chr8:52773000-52791200	Weak transcription	Thymus	Thymus
10	chr8:52773000-52803200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr8:52773600-52797000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:52773600-52797200	Weak transcription	Placenta	Placenta
13	chr8:52779400-52796200	Weak transcription	Brain Germinal Matrix	brain
14	chr8:52779400-52809000	Weak transcription	Fetal Kidney	kidney
15	chr8:52780400-52796400	Weak transcription	Liver	Liver
16	chr8:52780800-52803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr8:52781000-52791200	Weak transcription	Fetal Lung	lung
18	chr8:52781000-52793400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr8:52781200-52790600	Weak transcription	Fetal Intestine Small	intestine
20	chr8:52782200-52809600	Weak transcription	Aorta	Aorta
21	chr8:52782800-52791000	Weak transcription	Right Atrium	heart
22	chr8:52782800-52796200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:52783000-52791200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:52783000-52796800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:52783000-52797200	Weak transcription	HSMM	muscle
26	chr8:52783000-52803200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr8:52783000-52803400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr8:52783000-52803600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:52783200-52791000	Weak transcription	Adipose Nuclei	Adipose
30	chr8:52783200-52795800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr8:52783200-52796400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr8:52783200-52797200	Weak transcription	Fetal Brain Female	brain
33	chr8:52783400-52796600	Weak transcription	NHEK	skin
34	chr8:52783400-52796800	Weak transcription	Fetal Intestine Large	intestine
35	chr8:52783400-52797000	Weak transcription	Fetal Muscle Leg	muscle
36	chr8:52783600-52791400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr8:52783800-52791600	Weak transcription	Osteobl	bone
38	chr8:52784000-52791400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:52784000-52793000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr8:52784000-52795600	Weak transcription	Brain Hippocampus Middle	brain
41	chr8:52784000-52795800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:52784000-52797000	Weak transcription	HMEC	breast
43	chr8:52784000-52797000	Weak transcription	NH-A	brain
44	chr8:52784000-52806600	Weak transcription	Hela-S3	cervix
45	chr8:52784200-52790800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr8:52784200-52791400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr8:52784200-52794400	Weak transcription	K562	blood
48	chr8:52784200-52796200	Weak transcription	Brain Substantia Nigra	brain
49	chr8:52784200-52796800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr8:52784200-52796800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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