Variant report

Variant	rs10489686
Chromosome Location	chr1:192984059-192984060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:192762496..192765465-chr1:192982382..192985012,2	K562	blood:
2	chr1:192979947..192982887-chr1:192983438..192986734,3	K562	blood:
3	chr1:192980684..192984723-chr1:192984841..192989093,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10494675	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs10801170	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10801186	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs10921331	1.00[AFR][1000 genomes]
rs12118724	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12122868	0.85[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs12123511	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12123750	0.85[CEU][hapmap]
rs12123970	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129832	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132305	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12134846	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12135670	0.85[CEU][hapmap]
rs12136893	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12141029	0.85[CEU][hapmap]
rs12145101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs12145609	1.00[AFR][1000 genomes]
rs1325196	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17526825	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17592121	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17593120	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs17593414	1.00[AFR][1000 genomes]
rs2887640	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28930673	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs28930674	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs35221108	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56022114	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6670264	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6682904	0.85[CEU][hapmap]
rs6685991	1.00[AFR][1000 genomes]
rs72738588	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72738599	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72740243	1.00[AFR][1000 genomes]
rs72740246	1.00[AFR][1000 genomes]
rs7544830	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999499	chr1:192909529-192998421	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv535252	chr1:192909529-192998421	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv498699	chr1:192970436-192993624	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv3966	chr1:192976457-193004886	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv947359	chr1:192980236-192987689	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:192954200-192991200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:192955800-192990600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:192956200-192988400	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:192962600-192986400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:192963800-192990000	Weak transcription	HMEC	breast
6	chr1:192963800-192994400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:192963800-192996200	Weak transcription	Fetal Lung	lung
8	chr1:192963800-193012400	Weak transcription	NHEK	skin
9	chr1:192963800-193019600	Weak transcription	Ovary	ovary
10	chr1:192964000-192984600	Weak transcription	Primary B cells from cord blood	blood
11	chr1:192964000-192990400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:192964000-192994400	Weak transcription	Left Ventricle	heart
13	chr1:192965000-192990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:192966200-192994200	Weak transcription	Primary T cells from cord blood	blood
15	chr1:192966400-192985200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:192967600-192993000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:192968000-192984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:192968000-192992000	Weak transcription	Placenta	Placenta
19	chr1:192968000-193009400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:192968000-193012400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:192968000-193019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:192972800-192991200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:192972800-192991200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:192973200-192992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:192975200-192985000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:192975400-192991200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:192977600-192985200	Weak transcription	Dnd41	blood
28	chr1:192977600-192992000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:192977600-193005200	Weak transcription	A549	lung
30	chr1:192979000-192990600	Weak transcription	Liver	Liver
31	chr1:192979000-192994400	Weak transcription	HepG2	liver
32	chr1:192979200-193025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:192979800-192985000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:192979800-192989400	Weak transcription	GM12878-XiMat	blood
35	chr1:192980600-192990600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:192981200-192994600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:192981400-192994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:192981400-193026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:192981600-192984200	Enhancers	NHLF	lung
40	chr1:192981600-192984600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:192981800-192988400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:192982000-192984200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:192982200-192984200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:192982200-192985200	Weak transcription	HSMM	muscle
45	chr1:192982200-192991200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:192982400-192996400	Weak transcription	Fetal Intestine Small	intestine
47	chr1:192982600-192985000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:192982600-192987600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:192982600-192988200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:192982600-192988400	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links