Variant report

Variant	rs28657585
Chromosome Location	chr3:48736216-48736217
allele	A/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	chr3:48736187-48736469	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:48736167-48736450	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:48736158-48736680	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:48735966-48736432	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48736074-48736612	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:48736115-48736588	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48725665..48728051-chr3:48734995..48736912,2	MCF-7	breast:
2	chr3:48735352..48738114-chr3:48738712..48740970,2	K562	blood:

Variant related genes	Relation type
IP6K2	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10865952	0.95[ASN][1000 genomes]
rs11557629	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708786	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715177	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.81[ASN][1000 genomes]
rs11719291	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719457	0.80[AMR][1000 genomes]
rs12493578	0.95[ASN][1000 genomes]
rs12497850	0.95[ASN][1000 genomes]
rs12715429	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13063223	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070798	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13076269	0.81[AMR][1000 genomes]
rs13086240	0.84[AMR][1000 genomes]
rs13090013	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090839	0.80[AMR][1000 genomes]
rs13096357	0.81[AMR][1000 genomes]
rs13316551	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324119	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13324950	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	0.95[ASN][1000 genomes]
rs17080319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286651	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2286652	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2302295	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28452701	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28567949	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096717	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34153629	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577723	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3821875	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4077495	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[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	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61137521	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768448	0.83[EUR][1000 genomes]
rs6773261	0.81[AMR][1000 genomes]
rs6788650	0.95[ASN][1000 genomes]
rs68042649	0.83[EUR][1000 genomes]
rs7633840	0.86[ASN][1000 genomes]
rs9809222	0.83[EUR][1000 genomes]
rs9811027	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.83[EUR][1000 genomes]
rs9812200	0.81[EUR][1000 genomes]
rs9812977	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9821797	0.83[EUR][1000 genomes]
rs9834996	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836462	0.83[EUR][1000 genomes]
rs9841602	0.83[EUR][1000 genomes]
rs9848203	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9854034	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873726	0.83[EUR][1000 genomes]
rs9877542	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882549	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
rs28657585	WDR6	cis	Whole Blood	GTEx
rs28657585	WDR6	cis	lung	GTEx
rs28657585	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs28657585	WDR6	cis	Esophagus Mucosa	GTEx
rs28657585	WDR6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48724600-48738000	Strong transcription	Thymus	Thymus
2	chr3:48724600-48738400	Strong transcription	Primary hematopoietic stem cells	blood
3	chr3:48724600-48740400	Strong transcription	Primary B cells from cord blood	blood
4	chr3:48724600-48746600	Strong transcription	Fetal Thymus	thymus
5	chr3:48724600-48749000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48724800-48737600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:48724800-48738400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:48725000-48738600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:48725000-48738600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:48725000-48740400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:48725000-48740800	Strong transcription	Dnd41	blood
12	chr3:48725200-48738600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:48725200-48746200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:48732400-48736400	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr3:48732800-48744800	Weak transcription	Small Intestine	intestine
16	chr3:48732800-48745400	Weak transcription	Psoas Muscle	Psoas
17	chr3:48733000-48736400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:48733000-48740200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:48733000-48744800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:48733000-48745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:48733000-48753400	Weak transcription	Aorta	Aorta
22	chr3:48733200-48736800	Weak transcription	Colonic Mucosa	Colon
23	chr3:48733200-48737600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:48733200-48738600	Strong transcription	Fetal Lung	lung
25	chr3:48733200-48738800	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:48733200-48740800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:48733200-48744000	Weak transcription	Esophagus	oesophagus
28	chr3:48733200-48746000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:48733200-48746000	Strong transcription	Fetal Intestine Small	intestine
30	chr3:48733200-48746200	Weak transcription	Right Ventricle	heart
31	chr3:48733600-48739200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:48734000-48737400	Strong transcription	HSMMtube	muscle
33	chr3:48734000-48737600	Strong transcription	NH-A	brain
34	chr3:48734000-48737800	Strong transcription	HSMM	muscle
35	chr3:48734000-48738000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:48734000-48738600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr3:48734000-48746400	Weak transcription	Fetal Brain Male	brain
38	chr3:48734200-48736400	Weak transcription	Right Atrium	heart
39	chr3:48734200-48740200	Weak transcription	Fetal Heart	heart
40	chr3:48734200-48745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:48734400-48736400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:48734400-48736400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:48734400-48736600	Weak transcription	Ovary	ovary
44	chr3:48734400-48737000	Weak transcription	HMEC	breast
45	chr3:48734400-48737800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:48734400-48737800	Weak transcription	Brain Angular Gyrus	brain
47	chr3:48734400-48739800	Weak transcription	A549	lung
48	chr3:48734400-48740200	Weak transcription	NHDF-Ad	bronchial
49	chr3:48734400-48740800	Strong transcription	Fetal Intestine Large	intestine
50	chr3:48734400-48741600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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