Variant report

Variant	rs16916856
Chromosome Location	chr8:52739150-52739151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10087958	0.82[JPT][hapmap]
rs10504130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958300	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958301	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10958305	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11775587	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11775611	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11777016	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11777714	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11778849	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780040	0.98[ASN][1000 genomes]
rs11780891	0.95[AMR][1000 genomes]
rs11781330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784869	0.94[ASN][1000 genomes]
rs11785805	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs11786167	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11787229	0.86[ASN][1000 genomes]
rs12675786	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675907	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12676345	0.89[ASN][1000 genomes]
rs12676780	0.93[ASN][1000 genomes]
rs12676835	0.94[ASN][1000 genomes]
rs12677407	0.94[ASN][1000 genomes]
rs12678639	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12678680	0.88[AMR][1000 genomes]
rs12679287	0.94[ASN][1000 genomes]
rs12679983	0.88[ASN][1000 genomes]
rs12680128	0.88[ASN][1000 genomes]
rs12681203	0.94[ASN][1000 genomes]
rs12681734	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs13265006	0.98[ASN][1000 genomes]
rs13276400	0.89[ASN][1000 genomes]
rs16916820	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16916906	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16916961	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17212214	0.94[ASN][1000 genomes]
rs17212256	0.94[ASN][1000 genomes]
rs17284746	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs2037138	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037139	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2069119	0.89[ASN][1000 genomes]
rs2176120	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34058697	0.95[ASN][1000 genomes]
rs34073804	0.90[ASN][1000 genomes]
rs34213209	0.89[ASN][1000 genomes]
rs34319820	0.90[ASN][1000 genomes]
rs34364864	1.00[ASN][1000 genomes]
rs34372756	0.94[ASN][1000 genomes]
rs34677273	0.94[ASN][1000 genomes]
rs34973406	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35032384	0.94[ASN][1000 genomes]
rs35509250	0.89[ASN][1000 genomes]
rs35603537	0.89[ASN][1000 genomes]
rs41453644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4292674	0.88[ASN][1000 genomes]
rs4321994	0.87[ASN][1000 genomes]
rs4534123	0.88[ASN][1000 genomes]
rs4598243	0.96[ASN][1000 genomes]
rs4626585	0.88[ASN][1000 genomes]
rs57212480	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58561048	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58583070	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59602923	0.94[ASN][1000 genomes]
rs60153173	0.90[ASN][1000 genomes]
rs60304457	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60796336	0.94[ASN][1000 genomes]
rs61326367	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6994203	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71513549	0.88[ASN][1000 genomes]
rs71513552	0.90[ASN][1000 genomes]
rs71513561	0.98[ASN][1000 genomes]
rs71513564	0.94[ASN][1000 genomes]
rs763550	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650179	0.94[ASN][1000 genomes]
rs9650180	0.94[ASN][1000 genomes]
rs9650305	0.94[ASN][1000 genomes]
rs9792352	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3344694	chr8:52737249-52739247	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16916856	PCMTD1	trans	brain	seeQTL
rs16916856	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL
rs16916856	LOC115294	cis	multi-tissue	Pritchard
rs16916856	PCMTD1	cis	brain	seeQTL

Chromatin state (count:117 , 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	chr8:52721000-52741000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr8:52722000-52771400	Weak transcription	Gastric	stomach
5	chr8:52722200-52752000	Weak transcription	Pancreas	Pancrea
6	chr8:52722400-52741800	Weak transcription	Right Ventricle	heart
7	chr8:52722800-52741000	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:52722800-52741800	Weak transcription	HSMMtube	muscle
9	chr8:52723000-52741600	Weak transcription	Fetal Heart	heart
10	chr8:52726000-52741800	Weak transcription	Brain Substantia Nigra	brain
11	chr8:52727600-52756800	Weak transcription	Brain Angular Gyrus	brain
12	chr8:52728200-52759200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr8:52729800-52741600	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr8:52731400-52753400	Weak transcription	NHDF-Ad	bronchial
17	chr8:52731800-52741800	Weak transcription	Psoas Muscle	Psoas
18	chr8:52731800-52745600	Weak transcription	NHEK	skin
19	chr8:52732200-52743600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:52732200-52746000	Weak transcription	Fetal Brain Male	brain
21	chr8:52732200-52746400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr8:52732800-52753600	Weak transcription	Osteobl	bone
23	chr8:52733200-52741000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr8:52733200-52742600	Weak transcription	HepG2	liver
25	chr8:52733200-52758800	Weak transcription	Small Intestine	intestine
26	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:52733400-52739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr8:52733400-52741800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:52733400-52757200	Weak transcription	Colonic Mucosa	Colon
31	chr8:52733600-52745200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr8:52733800-52742000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
34	chr8:52734000-52742600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr8:52734400-52745200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr8:52735400-52741800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr8:52735400-52741800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr8:52735400-52741800	Weak transcription	Lung	lung
40	chr8:52735400-52744600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr8:52735400-52753400	Weak transcription	HUVEC	blood vessel
42	chr8:52735600-52740000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr8:52735600-52741200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:52735600-52741400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr8:52735600-52741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr8:52735600-52741800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr8:52735600-52753800	Weak transcription	HSMM	muscle
48	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
50	chr8:52735800-52739600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links