Variant report

Variant	rs952160
Chromosome Location	chr16:71965725-71965726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71961957..71964879-chr16:71965668..71968577,3	K562	blood:
2	chr16:71945578..71947499-chr16:71964859..71966489,2	MCF-7	breast:
3	chr16:71927384..71929645-chr16:71963039..71965792,3	MCF-7	breast:
4	chr16:71965319..71967704-chr16:72042287..72045013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102967	Chromatin interaction
ENSG00000263320	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1035543	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852506	0.88[ASN][1000 genomes]
rs10852508	0.85[ASN][1000 genomes]
rs12051425	0.82[GIH][hapmap]
rs12447423	0.85[ASN][1000 genomes]
rs12447856	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs12598902	0.83[YRI][hapmap]
rs12600153	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12600163	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12925901	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12930206	0.89[TSI][hapmap]
rs13332113	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13332180	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13337118	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549292	0.82[CHD][hapmap]
rs16973500	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs17286411	0.82[ASW][hapmap];0.86[JPT][hapmap]
rs1834033	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036338	0.89[TSI][hapmap]
rs2270830	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2270831	0.81[ASW][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2278031	0.81[ASW][hapmap];0.89[TSI][hapmap]
rs2291947	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2303220	0.90[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2878406	0.85[ASN][1000 genomes]
rs34111614	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4462592	0.85[ASN][1000 genomes]
rs4538017	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4788448	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4788551	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4788558	0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4788567	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4788572	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4788574	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4788578	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788587	0.82[GIH][hapmap]
rs55702379	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56309616	0.85[EUR][1000 genomes]
rs58114621	0.85[ASN][1000 genomes]
rs58609735	0.80[ASN][1000 genomes]
rs60075093	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60740701	0.90[EUR][1000 genomes]
rs7204798	0.82[GIH][hapmap]
rs7350856	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052028	0.84[ASN][1000 genomes]
rs8060867	0.82[CEU][hapmap]
rs952159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889100	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921705	0.85[ASN][1000 genomes]
rs9925441	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9925684	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9929683	0.83[YRI][hapmap]
rs9936965	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9937626	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9939455	0.83[MEX][hapmap];0.89[TSI][hapmap]

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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
6	nsv516948	chr16:71965725-71988728	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs952160	TMEM208	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr16:71948800-71968800	Strong transcription	Dnd41	blood
4	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
5	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
8	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:71953200-71969600	Strong transcription	Liver	Liver
12	chr16:71953800-71966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr16:71953800-71969000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr16:71953800-71969600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:71954000-71969000	Strong transcription	GM12878-XiMat	blood
16	chr16:71954000-71969000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr16:71954000-71969400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:71954000-71969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:71954200-71968200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr16:71954200-71969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr16:71955000-71969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr16:71956800-71971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:71958000-71969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr16:71961000-71966000	Strong transcription	Primary T cells from cord blood	blood
25	chr16:71961200-71966400	Strong transcription	HepG2	liver
26	chr16:71961800-71969600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:71962000-71971200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr16:71962400-71967800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr16:71962600-71967600	Weak transcription	Colonic Mucosa	Colon
30	chr16:71962600-71967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr16:71962600-71967800	Weak transcription	Aorta	Aorta
32	chr16:71962600-71967800	Weak transcription	Pancreas	Pancrea
33	chr16:71962600-71969600	Strong transcription	Placenta	Placenta
34	chr16:71962600-71972000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:71963000-71967600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr16:71963200-71966200	Weak transcription	Spleen	Spleen
37	chr16:71963200-71966400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr16:71963200-71967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr16:71963200-71967800	Weak transcription	Gastric	stomach
40	chr16:71963200-71967800	Weak transcription	Lung	lung
41	chr16:71963200-71968400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr16:71963200-71972000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr16:71963200-71972800	Weak transcription	Right Ventricle	heart
44	chr16:71963400-71967000	Weak transcription	Brain Substantia Nigra	brain
45	chr16:71963400-71967200	Weak transcription	Brain Hippocampus Middle	brain
46	chr16:71963400-71967600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr16:71963400-71968000	Weak transcription	Brain Angular Gyrus	brain
48	chr16:71963400-71969600	Strong transcription	Adipose Nuclei	Adipose
49	chr16:71963600-71965800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr16:71963600-71966200	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links