Variant report

Variant	rs3826153
Chromosome Location	chr16:69724223-69724224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10517	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs10852459	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1142105	0.84[ASN][1000 genomes]
rs12921017	0.86[ASN][1000 genomes]
rs13329844	0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs13331071	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13331216	0.82[ASN][1000 genomes]
rs13335149	0.82[ASN][1000 genomes]
rs13335664	0.82[ASN][1000 genomes]
rs13336317	1.00[MEX][hapmap]
rs16958997	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs16959059	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2304526	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2917665	0.82[ASN][1000 genomes]
rs2917667	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs2917669	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs2917673	0.87[ASN][1000 genomes]
rs2917674	0.87[ASN][1000 genomes]
rs2917675	0.83[ASN][1000 genomes]
rs2917676	0.87[ASN][1000 genomes]
rs2917679	0.82[ASN][1000 genomes]
rs2917682	0.86[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs2917683	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs2937125	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2965752	0.85[ASN][1000 genomes]
rs2965753	0.86[CHB][hapmap];0.92[CHD][hapmap]
rs2965757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2965758	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3785075	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs3826154	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs4502210	0.82[ASN][1000 genomes]
rs4985547	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6499246	0.81[ASN][1000 genomes]
rs689452	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs689456	0.85[ASN][1000 genomes]
rs7200420	0.86[ASN][1000 genomes]
rs7359387	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs9888993	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs9889219	0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs9921652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9924271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9924953	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs9925037	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs9927809	0.84[ASN][1000 genomes]
rs9934264	0.82[ASN][1000 genomes]
rs9934321	0.85[ASN][1000 genomes]
rs9934681	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs9936464	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs9937018	0.90[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs9938717	0.85[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	54 gene(s)	inside rSNPs	diseases
3	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3826153	CDH16	cis	cerebellum	SCAN
rs3826153	C16orf86	cis	parietal	SCAN
rs3826153	AP1G1	cis	parietal	SCAN
rs3826153	NOL3	cis	cerebellum	SCAN
rs3826153	ATP6V0D1	cis	cerebellum	SCAN
rs3826153	HYDIN	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:69681600-69725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:69681600-69725800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:69685000-69724800	Weak transcription	Fetal Heart	heart
6	chr16:69688600-69725400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:69690200-69725800	Weak transcription	Ovary	ovary
8	chr16:69691000-69726400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:69694800-69725800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr16:69700400-69725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:69701400-69725600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:69704000-69725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:69704600-69737800	Strong transcription	Liver	Liver
15	chr16:69705800-69725800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:69705800-69725800	Weak transcription	Gastric	stomach
17	chr16:69705800-69725800	Weak transcription	Small Intestine	intestine
18	chr16:69705800-69726000	Weak transcription	Psoas Muscle	Psoas
19	chr16:69706000-69725000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:69706000-69726200	Weak transcription	Stomach Mucosa	stomach
21	chr16:69706200-69725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:69706200-69725800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:69706200-69725800	Weak transcription	Right Ventricle	heart
24	chr16:69706400-69725800	Weak transcription	Brain Angular Gyrus	brain
25	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
26	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr16:69709600-69724600	Strong transcription	Fetal Intestine Large	intestine
29	chr16:69709600-69726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr16:69709800-69737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:69710000-69737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:69710800-69732000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr16:69711600-69725600	Weak transcription	Fetal Brain Male	brain
34	chr16:69712800-69725800	Weak transcription	Brain Germinal Matrix	brain
35	chr16:69712800-69725800	Weak transcription	Brain Substantia Nigra	brain
36	chr16:69713000-69724800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr16:69713200-69724400	Weak transcription	Colonic Mucosa	Colon
38	chr16:69713400-69725800	Weak transcription	Esophagus	oesophagus
39	chr16:69713400-69725800	Weak transcription	Thymus	Thymus
40	chr16:69713600-69724800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:69713800-69724400	Weak transcription	Colon Smooth Muscle	Colon
42	chr16:69713800-69725000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr16:69713800-69725800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:69714400-69725800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr16:69714600-69725600	Weak transcription	Brain Hippocampus Middle	brain
46	chr16:69714800-69724800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr16:69714800-69725600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr16:69715200-69737800	Strong transcription	HepG2	liver
49	chr16:69715600-69725800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr16:69716000-69724800	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links