Variant report

Variant	rs390802
Chromosome Location	chr3:52431671-52431672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52409891..52412947-chr3:52429055..52433083,4	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1011062	1.00[JPT][hapmap]
rs1011063	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs1011064	1.00[JPT][hapmap]
rs10461027	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs1077142	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865972	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11705963	0.94[EUR][1000 genomes]
rs11706001	0.93[EUR][1000 genomes]
rs11706108	0.94[EUR][1000 genomes]
rs11707864	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs11707931	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11709658	0.86[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11711934	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714402	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11716017	0.86[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11718125	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11721286	1.00[JPT][hapmap]
rs123598	1.00[JPT][hapmap]
rs123602	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13075370	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13091360	1.00[JPT][hapmap]
rs13091545	0.93[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs1541495	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs164637	1.00[JPT][hapmap]
rs17052058	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17052061	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17052068	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2016575	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2109558	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109559	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2159607	0.93[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2215466	1.00[JPT][hapmap]
rs2335640	0.93[CEU][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs28481563	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34238085	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34261027	0.86[EUR][1000 genomes]
rs34355561	0.94[EUR][1000 genomes]
rs34523877	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34551211	1.00[JPT][hapmap]
rs34762015	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs34908451	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35133416	0.93[EUR][1000 genomes]
rs352142	1.00[JPT][hapmap]
rs352143	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs352144	1.00[JPT][hapmap]
rs353548	1.00[JPT][hapmap]
rs35860312	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3752819	0.94[EUR][1000 genomes]
rs3774409	1.00[JPT][hapmap]
rs3774410	1.00[JPT][hapmap]
rs3796343	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs409803	0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	1.00[JPT][hapmap]
rs4687614	1.00[JPT][hapmap]
rs4687617	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4687618	1.00[JPT][hapmap]
rs4687619	1.00[JPT][hapmap]
rs498778	1.00[JPT][hapmap]
rs498946	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965068	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55997317	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56357549	0.93[EUR][1000 genomes]
rs57441156	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59612757	0.93[EUR][1000 genomes]
rs61150019	0.93[EUR][1000 genomes]
rs613519	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs634382	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445386	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445486	1.00[JPT][hapmap]
rs6445506	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs66462821	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67248391	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap]
rs6763882	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs6771558	1.00[JPT][hapmap]
rs67834575	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6784615	1.00[JPT][hapmap]
rs6794675	0.90[EUR][1000 genomes]
rs6796333	0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6800707	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6810027	1.00[JPT][hapmap]
rs728408	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs758803	1.00[JPT][hapmap]
rs7620015	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7643570	0.81[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs82825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887514	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs887515	0.93[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs929528	1.00[JPT][hapmap]
rs9844183	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9846089	1.00[JPT][hapmap]
rs9855470	1.00[JPT][hapmap]
rs9861879	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9863753	1.00[JPT][hapmap]
rs9867823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs390802	LOC286359	trans	parietal	SCAN
rs390802	SEMA3G	cis	cerebellum	SCAN
rs390802	DNAH1	cis	cerebellum	SCAN
rs390802	DNAH1	cis	parietal	SCAN
rs390802	ITIH3	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
2	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
4	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
5	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
9	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:52413800-52433000	Weak transcription	Fetal Brain Female	brain
13	chr3:52414000-52433200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
15	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
17	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
18	chr3:52419000-52441800	Strong transcription	Liver	Liver
19	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
20	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:52419200-52435400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
23	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
24	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:52419600-52432800	Weak transcription	Fetal Thymus	thymus
26	chr3:52419600-52435600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:52420000-52442000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
31	chr3:52422600-52441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:52423600-52434200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:52425600-52442000	Strong transcription	Spleen	Spleen
34	chr3:52426200-52436000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:52426400-52432000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:52426600-52442200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:52427400-52433000	Weak transcription	Right Ventricle	heart
38	chr3:52427400-52434600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:52427600-52432800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:52427600-52433600	Weak transcription	Stomach Mucosa	stomach
41	chr3:52427600-52433800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:52427600-52434000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:52427600-52434200	Weak transcription	Aorta	Aorta
44	chr3:52427800-52432800	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:52427800-52432800	Weak transcription	Thymus	Thymus
46	chr3:52427800-52434000	Weak transcription	Left Ventricle	heart
47	chr3:52427800-52436000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:52428200-52432800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:52428200-52433200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:52428200-52433400	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links