Variant report

Variant	rs36100144
Chromosome Location	chr8:52757353-52757354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13250133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13253956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13262316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13263610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13263767	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13264394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13267912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13270817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13272813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13274476	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13277070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13279973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17196182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17196300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17196343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17210431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17210466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17282351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34011046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34070508	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34152859	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34424720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34461077	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34724314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34837796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34934450	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34949360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35025549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35038146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35098517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35254751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35314611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35448466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35822658	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35918180	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35933421	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71513545	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71513547	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71513550	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71513551	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71513553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71513558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71513559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71513560	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71513562	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71513563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[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
rs36100144	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52722000-52771400	Weak transcription	Gastric	stomach
2	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:52733200-52758800	Weak transcription	Small Intestine	intestine
6	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
9	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
12	chr8:52735800-52763400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:52737200-52760400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:52739800-52765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr8:52739800-52782600	Weak transcription	K562	blood
16	chr8:52742000-52765400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:52742600-52763400	Weak transcription	Brain Substantia Nigra	brain
18	chr8:52743000-52757600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr8:52743000-52771400	Weak transcription	HepG2	liver
20	chr8:52743200-52765400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr8:52743400-52758800	Weak transcription	Brain Anterior Caudate	brain
22	chr8:52743400-52763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr8:52743400-52766200	Weak transcription	HSMMtube	muscle
24	chr8:52743400-52771400	Weak transcription	Esophagus	oesophagus
25	chr8:52743600-52758800	Weak transcription	Spleen	Spleen
26	chr8:52743800-52758600	Weak transcription	Left Ventricle	heart
27	chr8:52743800-52758800	Weak transcription	Lung	lung
28	chr8:52743800-52763000	Weak transcription	Fetal Kidney	kidney
29	chr8:52743800-52763600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:52743800-52765200	Weak transcription	Brain Hippocampus Middle	brain
31	chr8:52744000-52758800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr8:52744000-52763000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:52744000-52763600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr8:52744000-52768200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:52744000-52771200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:52744000-52771400	Weak transcription	Fetal Brain Female	brain
37	chr8:52744200-52770800	Weak transcription	Placenta	Placenta
38	chr8:52744400-52768600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr8:52744600-52762400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr8:52744600-52769000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:52744600-52769200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr8:52744800-52758600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr8:52745600-52768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:52745800-52758800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr8:52745800-52762600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr8:52745800-52765400	Weak transcription	Thymus	Thymus
47	chr8:52745800-52769400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr8:52746000-52762200	Weak transcription	Liver	Liver
49	chr8:52746000-52763000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr8:52746000-52765600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links