Variant report

Variant	rs9390200
Chromosome Location	chr6:145028992-145028993
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13199226	0.91[AMR][1000 genomes]
rs1406045	0.82[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes]
rs1534439	0.88[AMR][1000 genomes]
rs1590054	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2328598	0.89[AMR][1000 genomes]
rs2328600	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4895649	0.88[AMR][1000 genomes]
rs6570641	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6906948	0.91[GIH][hapmap]
rs6924941	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6927255	0.87[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes]
rs7750326	0.91[GIH][hapmap]
rs7758449	0.80[AMR][1000 genomes]
rs9321987	0.91[ASW][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs9373423	0.81[AMR][1000 genomes]
rs9376843	0.92[AMR][1000 genomes]
rs9390189	0.83[AMR][1000 genomes]
rs9390197	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs9390201	0.89[GIH][hapmap]
rs9403587	0.81[CEU][hapmap]
rs9484899	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1021098	chr6:145017386-145106441	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9390200	VCAN	trans	lymphoblastoid	seeQTL
rs9390200	EPM2A	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144981200-145031000	Weak transcription	Placenta	Placenta
2	chr6:144996600-145052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:145004400-145047000	Weak transcription	HSMMtube	muscle
4	chr6:145005000-145031000	Weak transcription	HUVEC	blood vessel
5	chr6:145009000-145029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:145009000-145047000	Weak transcription	Esophagus	oesophagus
7	chr6:145010400-145029600	Weak transcription	Aorta	Aorta
8	chr6:145010600-145047000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:145010800-145031000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:145010800-145031400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:145011000-145052600	Weak transcription	Ovary	ovary
12	chr6:145011200-145029600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:145011200-145035200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:145011800-145031000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:145011800-145065600	Weak transcription	Pancreas	Pancrea
16	chr6:145011800-145090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:145011800-145096600	Weak transcription	Thymus	Thymus
18	chr6:145012000-145029400	Weak transcription	Lung	lung
19	chr6:145012000-145036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:145012000-145039200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:145012000-145047000	Weak transcription	Gastric	stomach
22	chr6:145012000-145055600	Weak transcription	Spleen	Spleen
23	chr6:145012400-145053000	Weak transcription	Fetal Stomach	stomach
24	chr6:145013800-145031200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:145014200-145033600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:145014200-145047000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:145017600-145029800	Weak transcription	GM12878-XiMat	blood
28	chr6:145018200-145031000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:145018200-145047200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:145018200-145052400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:145018400-145031200	Weak transcription	NHLF	lung
32	chr6:145018400-145069000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:145018600-145031000	Weak transcription	NHDF-Ad	bronchial
34	chr6:145018800-145029400	Weak transcription	Fetal Intestine Large	intestine
35	chr6:145018800-145033400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:145018800-145041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:145019000-145031200	Weak transcription	Osteobl	bone
38	chr6:145019000-145047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:145019200-145032000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:145019400-145036600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:145019400-145052600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:145019800-145031200	Weak transcription	NH-A	brain
43	chr6:145020200-145035400	Weak transcription	Fetal Lung	lung
44	chr6:145020600-145030200	Strong transcription	Dnd41	blood
45	chr6:145020800-145039400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:145021200-145030200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:145021200-145031800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr6:145021200-145032000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:145021200-145032000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:145021400-145031400	Weak transcription	H9 Cell Line	embryonic stem cell

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