Variant report

Variant	rs9877542
Chromosome Location	chr3:48748545-48748546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11708786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.84[AMR][1000 genomes]
rs11715177	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493578	0.95[ASN][1000 genomes]
rs12497850	0.95[ASN][1000 genomes]
rs12715429	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13063223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13073997	0.84[AMR][1000 genomes]
rs13074318	0.84[AMR][1000 genomes]
rs13084000	0.84[AMR][1000 genomes]
rs13087930	0.84[AMR][1000 genomes]
rs13090013	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13324950	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	0.95[ASN][1000 genomes]
rs17080319	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2286652	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2302295	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28452701	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28567949	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34153629	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3821875	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4077495	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	0.95[ASN][1000 genomes]
rs4858828	0.95[ASN][1000 genomes]
rs4858831	0.95[ASN][1000 genomes]
rs56735597	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61137521	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs6768448	0.82[EUR][1000 genomes]
rs6788650	0.95[ASN][1000 genomes]
rs68042649	0.82[EUR][1000 genomes]
rs71324924	0.84[AMR][1000 genomes]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.82[EUR][1000 genomes]
rs9811027	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.82[EUR][1000 genomes]
rs9821797	0.82[EUR][1000 genomes]
rs9834996	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836462	0.82[EUR][1000 genomes]
rs9841602	0.82[EUR][1000 genomes]
rs9848203	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	0.82[EUR][1000 genomes]
rs9877685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9877542	WDR6	cis	Adipose Subcutaneous	GTEx
rs9877542	WDR6	cis	Esophagus Mucosa	GTEx
rs9877542	WDR6	cis	Whole Blood	GTEx
rs9877542	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9877542	WDR6	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
3	chr3:48734400-48748800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:48738200-48752400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:48739800-48750800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:48740000-48753600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:48741400-48750600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:48741600-48749600	Strong transcription	Primary B cells from cord blood	blood
9	chr3:48741600-48750600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:48741600-48752400	Strong transcription	Fetal Intestine Large	intestine
11	chr3:48741800-48749400	Strong transcription	Fetal Stomach	stomach
12	chr3:48741800-48751800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:48741800-48752400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:48741800-48752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:48742000-48748800	Strong transcription	Thymus	Thymus
16	chr3:48742800-48750000	Strong transcription	Placenta	Placenta
17	chr3:48742800-48750800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:48743000-48749600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:48743000-48752400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:48743000-48753000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:48743600-48750600	Strong transcription	Hela-S3	cervix
22	chr3:48743600-48751200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:48743600-48751800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:48743600-48752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:48743800-48752800	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr3:48744600-48749400	Strong transcription	Liver	Liver
27	chr3:48744600-48749600	Strong transcription	HUVEC	blood vessel
28	chr3:48744600-48751000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:48744600-48751200	Genic enhancers	Primary T cells from cord blood	blood
30	chr3:48744800-48750600	Genic enhancers	Brain Germinal Matrix	brain
31	chr3:48745600-48751200	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr3:48745600-48752800	Weak transcription	Small Intestine	intestine
33	chr3:48745800-48753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:48746200-48748800	Strong transcription	Fetal Kidney	kidney
35	chr3:48746400-48748600	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:48746400-48749800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:48746600-48749200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:48746600-48752400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:48746600-48752400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:48746600-48752600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:48746800-48748600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:48746800-48748600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:48746800-48748600	Weak transcription	Fetal Brain Male	brain
44	chr3:48746800-48748600	Strong transcription	Lung	lung
45	chr3:48746800-48748600	Weak transcription	Ovary	ovary
46	chr3:48746800-48748800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:48746800-48748800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:48746800-48748800	Weak transcription	Stomach Mucosa	stomach
49	chr3:48746800-48749200	Strong transcription	Colonic Mucosa	Colon
50	chr3:48746800-48749200	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links