Variant report

Variant	rs9939458
Chromosome Location	chr16:71667131-71667132
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:71667059-71667234	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
MARVELD3	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1058750	1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852502	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852503	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075893	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11075894	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075898	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075901	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs11075904	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11075905	0.91[CEU][hapmap]
rs11862723	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12923990	0.84[EUR][1000 genomes]
rs12929547	1.00[ASN][1000 genomes]
rs1364210	1.00[ASN][1000 genomes]
rs1392484	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1423983	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032918	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052584	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052585	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113223	1.00[ASN][1000 genomes]
rs2133773	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247603	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2334877	0.90[CEU][hapmap]
rs2334880	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4354946	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788548	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788550	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788553	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788557	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788559	0.90[CEU][hapmap]
rs4788810	0.81[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788813	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788820	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788822	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788823	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788825	0.88[EUR][1000 genomes]
rs4788828	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788830	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499526	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499527	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499528	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499529	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499530	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499531	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499534	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499538	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499540	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7186112	1.00[ASN][1000 genomes]
rs7187948	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7188675	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7190487	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193549	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7201649	0.80[EUR][1000 genomes]
rs7202479	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204608	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204967	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204992	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206470	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7359478	1.00[ASN][1000 genomes]
rs8044144	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8051968	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052910	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053186	1.00[ASN][1000 genomes]
rs8053745	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055419	0.81[EUR][1000 genomes]
rs8058297	0.96[EUR][1000 genomes]
rs8062188	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889568	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635524	1.00[ASN][1000 genomes]
rs979790	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888756	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929840	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9929985	1.00[ASN][1000 genomes]
rs9930015	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs9931074	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934301	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934789	0.87[EUR][1000 genomes]
rs9937511	1.00[ASN][1000 genomes]

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	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	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9939458	PHLPP2	cis	Muscle Skeletal	GTEx
rs9939458	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71661000-71671000	Weak transcription	Right Atrium	heart
2	chr16:71661000-71674200	Weak transcription	Gastric	stomach
3	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:71662000-71674200	Weak transcription	Lung	lung
5	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr16:71662800-71673600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr16:71663000-71669600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr16:71663000-71670800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:71663200-71668600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:71663200-71670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:71663200-71670600	Weak transcription	Osteobl	bone
13	chr16:71663200-71670800	Weak transcription	Ovary	ovary
14	chr16:71663200-71671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr16:71663200-71673800	Weak transcription	Brain Hippocampus Middle	brain
16	chr16:71663200-71676800	Weak transcription	Fetal Kidney	kidney
17	chr16:71663400-71668200	Weak transcription	Fetal Stomach	stomach
18	chr16:71663400-71668800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr16:71663400-71669200	Strong transcription	Fetal Intestine Small	intestine
20	chr16:71663400-71669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr16:71663400-71670000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr16:71663400-71674200	Weak transcription	Adipose Nuclei	Adipose
23	chr16:71663400-71674200	Weak transcription	Aorta	Aorta
24	chr16:71663400-71674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr16:71663400-71674400	Weak transcription	Esophagus	oesophagus
26	chr16:71663400-71678400	Weak transcription	Fetal Lung	lung
27	chr16:71663600-71668000	Weak transcription	Colonic Mucosa	Colon
28	chr16:71663600-71668600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:71663600-71686600	Weak transcription	Small Intestine	intestine
30	chr16:71663800-71667800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr16:71663800-71667800	Weak transcription	Pancreas	Pancrea
32	chr16:71663800-71669800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr16:71663800-71673800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr16:71663800-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr16:71663800-71680600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:71663800-71681400	Weak transcription	Left Ventricle	heart
37	chr16:71663800-71681400	Weak transcription	HepG2	liver
38	chr16:71664000-71667800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr16:71664000-71668000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:71664000-71669600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr16:71664000-71671000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr16:71664200-71667600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr16:71664200-71670400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:71664600-71682800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr16:71665000-71671000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:71665200-71673000	Strong transcription	Fetal Intestine Large	intestine
47	chr16:71665200-71673800	Weak transcription	Liver	Liver
48	chr16:71665200-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr16:71665200-71682800	Weak transcription	HMEC	breast
50	chr16:71665400-71667800	Weak transcription	NHEK	skin

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