Variant report

Variant	rs9395890
Chromosome Location	chr6:53820994-53820995
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:53593244..53593769-chr6:53820705..53821237,2	MCF-7	breast:
2	chr6:53583327..53584025-chr6:53820811..53821451,2	MCF-7	breast:
3	chr6:53819656..53822349-chr6:53824906..53826764,2	K562	blood:
4	chr6:53657866..53662110-chr6:53819817..53822603,6	MCF-7	breast:
5	chr5:82726389..82726918-chr6:53820685..53821483,2	MCF-7	breast:
6	chr6:53657156..53661556-chr6:53818484..53821227,4	MCF-7	breast:
7	chr6:53658805..53659598-chr6:53820598..53821414,3	MCF-7	breast:
8	chr6:53658811..53659800-chr6:53820598..53821505,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10456168	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10456676	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10755768	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10948790	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12190914	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437448	0.92[ASN][1000 genomes]
rs2006013	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050159	0.81[EUR][1000 genomes]
rs2206574	0.82[ASN][1000 genomes]
rs2397150	0.82[ASN][1000 genomes]
rs34299171	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4398734	0.87[ASN][1000 genomes]
rs4712050	0.91[ASN][1000 genomes]
rs4712051	0.92[ASN][1000 genomes]
rs5006063	0.93[ASN][1000 genomes]
rs6458973	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6902746	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906326	0.82[CEU][hapmap]
rs6907354	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6909052	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6909056	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6909350	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6916929	0.80[EUR][1000 genomes]
rs6927232	0.90[ASN][1000 genomes]
rs6928440	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935942	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs742525	0.87[ASN][1000 genomes]
rs7744962	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752981	0.82[ASN][1000 genomes]
rs7769351	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7773779	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296727	0.92[ASN][1000 genomes]
rs9357777	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357779	0.82[ASN][1000 genomes]
rs9367545	0.92[AMR][1000 genomes]
rs9367546	0.82[ASN][1000 genomes]
rs9370245	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395891	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9395892	0.90[AMR][1000 genomes]
rs9395893	0.87[ASN][1000 genomes]
rs9395894	0.87[ASN][1000 genomes]
rs9463996	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9463997	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9474671	0.80[EUR][1000 genomes]
rs9474680	0.80[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53795600-53826200	Weak transcription	NHEK	skin
2	chr6:53811400-53825000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:53819000-53827000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:53819400-53821400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:53820600-53821400	Enhancers	Dnd41	blood
6	chr6:53820600-53821400	Enhancers	Hela-S3	cervix
7	chr6:53820800-53821200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:53820800-53821400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:53820800-53821400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:53820800-53821400	Enhancers	Brain Substantia Nigra	brain
11	chr6:53820800-53821400	Enhancers	Fetal Thymus	thymus
12	chr6:53820800-53821400	Enhancers	A549	lung

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