Variant report

Variant	rs13074318
Chromosome Location	chr3:48816725-48816726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1048940	0.84[CEU][hapmap]
rs11706052	0.85[AMR][1000 genomes]
rs11706983	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs11708022	1.00[AMR][1000 genomes]
rs11708786	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs11709092	0.96[AMR][1000 genomes]
rs11709246	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11712006	0.85[AMR][1000 genomes]
rs11713694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715177	0.84[AMR][1000 genomes]
rs11715689	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715713	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715835	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717978	0.92[AMR][1000 genomes]
rs11718982	0.85[AMR][1000 genomes]
rs11719291	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs11719457	0.89[AMR][1000 genomes]
rs12107252	0.83[GIH][hapmap]
rs12107418	0.83[GIH][hapmap]
rs13063223	0.84[AMR][1000 genomes]
rs13063312	0.83[GIH][hapmap]
rs13063742	1.00[AFR][1000 genomes]
rs13069446	1.00[AFR][1000 genomes]
rs13070798	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs13072554	0.85[AMR][1000 genomes]
rs13073997	1.00[AMR][1000 genomes]
rs13080725	0.85[AMR][1000 genomes]
rs13084000	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13086240	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs13087930	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs13090839	0.89[AMR][1000 genomes]
rs13094900	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13324142	0.83[GIH][hapmap]
rs13324950	0.84[AMR][1000 genomes]
rs13434258	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs17080289	0.83[GIH][hapmap]
rs17080319	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2276850	0.83[GIH][hapmap]
rs2276852	0.83[GIH][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs2310996	0.83[GIH][hapmap]
rs28793701	0.84[AMR][1000 genomes]
rs34037363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34477108	1.00[AMR][1000 genomes]
rs34504524	0.85[AMR][1000 genomes]
rs34509487	1.00[AMR][1000 genomes]
rs34580506	0.85[AMR][1000 genomes]
rs35064573	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap]
rs35102816	0.85[AMR][1000 genomes]
rs35108630	0.85[AMR][1000 genomes]
rs35283189	0.85[AMR][1000 genomes]
rs3821876	0.83[GIH][hapmap]
rs3923475	0.85[AMR][1000 genomes]
rs4077495	0.84[AMR][1000 genomes]
rs55761431	0.85[AMR][1000 genomes]
rs56318350	0.90[AMR][1000 genomes]
rs56735597	0.84[AMR][1000 genomes]
rs61729488	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6442130	1.00[CHB][hapmap]
rs67060340	0.96[AMR][1000 genomes]
rs67332931	1.00[AMR][1000 genomes]
rs6792156	0.83[GIH][hapmap]
rs71324924	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71324929	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73078349	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73078362	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73080361	0.88[AMR][1000 genomes]
rs740787	0.83[GIH][hapmap]
rs7627404	1.00[CHB][hapmap]
rs7631574	0.83[GIH][hapmap]
rs9811027	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9811318	0.83[GIH][hapmap]
rs9812200	0.83[GIH][hapmap]
rs9830581	0.83[GIH][hapmap]
rs9834996	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs9835307	1.00[CHB][hapmap]
rs9836462	0.83[GIH][hapmap]
rs9841602	0.83[GIH][hapmap]
rs9843316	0.83[GIH][hapmap]
rs9877542	0.84[AMR][1000 genomes]
rs9877685	0.84[AMR][1000 genomes]
rs9882549	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][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	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs13074318	LRRC2	cis	cerebellum	SCAN
rs13074318	WDR6	cis	Whole Blood	GTEx
rs13074318	WDR6	cis	Artery Tibial	GTEx
rs13074318	WDR6	cis	lymphoblastoid	seeQTL
rs13074318	WDR6	cis	cerebellum	SCAN
rs13074318	WDR6	cis	parietal	SCAN
rs13074318	RNF123	cis	parietal	SCAN
rs13074318	ARIH2	cis	cerebellum	SCAN
rs13074318	ALAS1	cis	cerebellum	SCAN
rs13074318	CCDC71	cis	cerebellum	SCAN
rs13074318	CCDC36	cis	cerebellum	SCAN
rs13074318	HEMK1	cis	parietal	SCAN
rs13074318	NICN1	cis	cerebellum	SCAN
rs13074318	C3orf62	cis	cerebellum	SCAN
rs13074318	WDR6	cis	Adipose Subcutaneous	GTEx
rs13074318	KBTBD3	trans	parietal	SCAN
rs13074318	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs13074318	CSPG5	cis	parietal	SCAN
rs13074318	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13074318	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48778200-48820200	Weak transcription	Fetal Kidney	kidney
2	chr3:48778200-48836600	Weak transcription	A549	lung
3	chr3:48778600-48826000	Weak transcription	Stomach Mucosa	stomach
4	chr3:48785400-48819200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:48789400-48844000	Weak transcription	Fetal Lung	lung
6	chr3:48789600-48820200	Weak transcription	Fetal Brain Male	brain
7	chr3:48789600-48820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:48789600-48825800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:48789800-48819000	Weak transcription	Small Intestine	intestine
10	chr3:48790000-48819600	Weak transcription	NHLF	lung
11	chr3:48790200-48823600	Weak transcription	HMEC	breast
12	chr3:48791200-48825800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:48793200-48825800	Weak transcription	Fetal Thymus	thymus
14	chr3:48794800-48819600	Weak transcription	NHDF-Ad	bronchial
15	chr3:48795200-48819600	Weak transcription	Colonic Mucosa	Colon
16	chr3:48795200-48833600	Weak transcription	Psoas Muscle	Psoas
17	chr3:48797000-48823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:48802200-48832600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:48802600-48819600	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:48802800-48820400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:48807600-48822000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:48808000-48819600	Weak transcription	Esophagus	oesophagus
23	chr3:48808000-48819600	Weak transcription	Right Ventricle	heart
24	chr3:48808000-48822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:48808000-48825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:48808200-48819800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:48808200-48820000	Weak transcription	Aorta	Aorta
28	chr3:48808200-48820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:48808200-48821800	Weak transcription	HSMMtube	muscle
30	chr3:48808200-48827000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:48808400-48819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:48808400-48828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:48809000-48819400	Weak transcription	Spleen	Spleen
34	chr3:48809000-48819600	Weak transcription	Gastric	stomach
35	chr3:48809000-48849400	Weak transcription	GM12878-XiMat	blood
36	chr3:48809600-48819600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:48809600-48819800	Weak transcription	Ovary	ovary
38	chr3:48809600-48826200	Weak transcription	Primary B cells from cord blood	blood
39	chr3:48809800-48819400	Weak transcription	NH-A	brain
40	chr3:48809800-48819600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:48809800-48819600	Weak transcription	Brain Germinal Matrix	brain
42	chr3:48809800-48819800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:48810000-48819600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:48810000-48826000	Weak transcription	Brain Angular Gyrus	brain
45	chr3:48810000-48882800	Weak transcription	Fetal Brain Female	brain
46	chr3:48810200-48819200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:48810200-48819800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:48810200-48820000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:48810400-48817600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:48810400-48818800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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