Variant report

Variant	rs9399489
Chromosome Location	chr6:145002776-145002777
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11155364	0.86[GIH][hapmap];0.82[MEX][hapmap]
rs11155365	0.91[CEU][hapmap]
rs11155370	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12209027	0.91[CEU][hapmap];0.93[GIH][hapmap]
rs17074004	0.91[CEU][hapmap]
rs1980379	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs2056745	0.91[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs4895646	0.91[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs6907773	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9373420	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9376835	0.82[CHD][hapmap];0.83[GIH][hapmap]
rs9376837	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9376838	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9386076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390184	0.91[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap]
rs9390187	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9390188	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9399483	0.91[CEU][hapmap]
rs9399486	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9399488	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403578	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399489	STX11	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144981200-145031000	Weak transcription	Placenta	Placenta
2	chr6:144982800-145010000	Weak transcription	Fetal Stomach	stomach
3	chr6:144983000-145024600	Weak transcription	Fetal Kidney	kidney
4	chr6:144985000-145004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:144996000-145010000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:144996600-145004000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:144996600-145004000	Weak transcription	Thymus	Thymus
8	chr6:144996600-145004200	Weak transcription	HSMMtube	muscle
9	chr6:144996600-145007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:144996600-145018400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:144996600-145052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:144996800-145007400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:144996800-145009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:144997000-145004000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:144997000-145004200	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:144997000-145004200	Weak transcription	Gastric	stomach
17	chr6:144997000-145004200	Weak transcription	Pancreas	Pancrea
18	chr6:144997000-145004200	Weak transcription	Psoas Muscle	Psoas
19	chr6:144997000-145004200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:144997000-145004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:144997000-145006200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:144997000-145006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:144997000-145006600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:144997000-145008000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:144997000-145008000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:144997000-145008600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:144997000-145009400	Weak transcription	HMEC	breast
28	chr6:144997000-145010000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:144997000-145010000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:144997000-145010000	Weak transcription	Spleen	Spleen
31	chr6:144997000-145010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:144997000-145010200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:144997000-145010600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:144997000-145010600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:144997000-145011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:144997000-145011400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:144997000-145011800	Weak transcription	Colonic Mucosa	Colon
38	chr6:144997000-145017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:144997200-145018000	Weak transcription	NHLF	lung
40	chr6:144997800-145007400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:144998600-145007400	Weak transcription	GM12878-XiMat	blood
42	chr6:144999400-145003000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:144999400-145006200	Strong transcription	Primary B cells from cord blood	blood
44	chr6:144999400-145013200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:144999400-145025400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:144999600-145002800	Strong transcription	HepG2	liver
47	chr6:144999600-145003000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:144999600-145003200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr6:144999600-145007000	Strong transcription	Dnd41	blood
50	chr6:144999800-145004200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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