Variant report

Variant	rs9962435
Chromosome Location	chr18:12908488-12908489
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12902756..12905734-chr18:12905891..12908920,3	K562	blood:
2	chr18:12908308..12911481-chr18:12911721..12914247,3	MCF-7	breast:
3	chr18:12882774..12886006-chr18:12907131..12909300,4	K562	blood:
4	chr18:12871381..12873022-chr18:12906708..12908955,2	K562	blood:

Variant related genes	Relation type
ENSG00000267336	Chromatin interaction
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11080609	0.86[EUR][1000 genomes]
rs11080611	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1983424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34568924	0.87[ASN][1000 genomes]
rs3848468	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3915012	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs4796969	0.86[JPT][hapmap]
rs4797713	0.93[EUR][1000 genomes]
rs4797714	0.85[EUR][1000 genomes]
rs4797717	0.82[ASN][1000 genomes]
rs7242109	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089211	0.91[EUR][1000 genomes]
rs8090365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8092942	0.93[EUR][1000 genomes]
rs8094285	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12904200-12908600	Weak transcription	Left Ventricle	heart
2	chr18:12904400-12911200	Weak transcription	Spleen	Spleen
3	chr18:12904600-12910000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr18:12906200-12909200	Enhancers	Fetal Thymus	thymus
5	chr18:12906400-12909000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr18:12906800-12911000	Weak transcription	Right Ventricle	heart
7	chr18:12907000-12911000	Weak transcription	Gastric	stomach
8	chr18:12907400-12911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:12907400-12911200	Weak transcription	Lung	lung
10	chr18:12907600-12908600	Weak transcription	K562	blood
11	chr18:12907600-12908800	Weak transcription	Aorta	Aorta
12	chr18:12907600-12909000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:12907600-12909200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr18:12907600-12913600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr18:12907800-12909000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:12907800-12909000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:12908000-12908600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr18:12908200-12909200	Enhancers	Osteobl	bone
19	chr18:12908200-12911000	Weak transcription	Right Atrium	heart
20	chr18:12908400-12909000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr18:12908400-12911000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr18:12908400-12911200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links