Variant report

Variant	rs8055516
Chromosome Location	chr16:12180198-12180199
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11075049	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11639701	0.81[ASN][1000 genomes]
rs11642386	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11648228	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11648468	0.83[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11648816	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12596549	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12596703	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12599090	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12708745	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12708746	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12708747	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12926900	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs13330399	1.00[ASW][hapmap];0.84[CHB][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13331254	0.84[CHB][hapmap]
rs13333662	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs13336687	0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13338070	0.89[AFR][1000 genomes]
rs16958964	0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2175020	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2457193	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28439695	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28667047	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869808	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350264	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350265	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350266	0.89[ASN][1000 genomes]
rs35053871	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35318501	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3851011	0.94[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3851012	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3894905	0.81[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs4780411	0.84[ASN][1000 genomes]
rs4781180	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs71385189	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7195019	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7200307	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8048589	0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8050180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs8059989	0.86[ASN][1000 genomes]
rs8062015	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8063329	0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9925009	0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9939383	1.00[ASW][hapmap];0.80[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8055516	TNFRSF17	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr16:12146000-12183400	Weak transcription	Fetal Intestine Large	intestine
4	chr16:12148000-12183400	Weak transcription	Fetal Lung	lung
5	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
6	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
7	chr16:12157000-12181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr16:12157000-12181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:12157200-12183200	Weak transcription	NHLF	lung
10	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:12157800-12181400	Weak transcription	Right Ventricle	heart
12	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
13	chr16:12162200-12181400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr16:12163600-12181600	Weak transcription	Brain Substantia Nigra	brain
15	chr16:12163600-12183600	Weak transcription	Colon Smooth Muscle	Colon
16	chr16:12163800-12181600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr16:12167600-12185800	Weak transcription	HSMM	muscle
18	chr16:12170000-12183400	Weak transcription	HepG2	liver
19	chr16:12170200-12183400	Weak transcription	Colonic Mucosa	Colon
20	chr16:12170600-12182000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr16:12171400-12180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:12171600-12180200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr16:12173000-12180800	Weak transcription	Gastric	stomach
24	chr16:12173000-12181600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:12173000-12181600	Weak transcription	Esophagus	oesophagus
26	chr16:12173000-12181600	Weak transcription	Right Atrium	heart
27	chr16:12173400-12183200	Weak transcription	Liver	Liver
28	chr16:12173600-12182800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:12173600-12183400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:12173600-12183400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:12173800-12181400	Weak transcription	Brain Angular Gyrus	brain
32	chr16:12173800-12181600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr16:12173800-12183200	Weak transcription	Brain Hippocampus Middle	brain
34	chr16:12173800-12183400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr16:12173800-12183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr16:12174200-12181800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:12174200-12183000	Weak transcription	HUVEC	blood vessel
38	chr16:12174200-12183200	Weak transcription	Osteobl	bone
39	chr16:12174200-12183400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr16:12174400-12182000	Weak transcription	Spleen	Spleen
41	chr16:12174400-12182400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:12174400-12183200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr16:12175000-12181800	Weak transcription	Brain Anterior Caudate	brain
44	chr16:12175200-12185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr16:12175400-12183200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:12175600-12183200	Weak transcription	Fetal Intestine Small	intestine
47	chr16:12175600-12183400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr16:12175800-12183200	Weak transcription	NH-A	brain
49	chr16:12176000-12181800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr16:12176000-12181800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links