Variant report

Variant	rs10447854
Chromosome Location	chr7:127795804-127795805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127795407..127797844-chr7:127804124..127806542,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10254438	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269842	1.00[ASN][1000 genomes]
rs10447853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10447855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154534	1.00[ASN][1000 genomes]
rs12533765	1.00[ASN][1000 genomes]
rs12534062	1.00[ASN][1000 genomes]
rs12537331	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151707	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17151739	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17679136	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17679208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17735893	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17735958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28399051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558944	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28625157	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28692983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56340588	1.00[ASN][1000 genomes]
rs62484024	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484025	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484026	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484033	1.00[ASN][1000 genomes]
rs6962635	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6965344	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73226626	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238088	1.00[ASN][1000 genomes]
rs73239704	1.00[ASN][1000 genomes]
rs73239710	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10447854	OPN1SW	cis	cerebellum	SCAN
rs10447854	RBM28	cis	cerebellum	SCAN
rs10447854	KLHDC10	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127788600-127796000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr7:127790600-127803400	Weak transcription	Spleen	Spleen
3	chr7:127791400-127796000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr7:127793800-127796000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr7:127794000-127796000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:127794200-127796000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:127794200-127796000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:127794400-127796000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr7:127794400-127796000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr7:127794400-127796000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:127794600-127796000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr7:127794600-127796000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:127794800-127796000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:127795000-127796000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr7:127795200-127796000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:127795200-127796000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr7:127795200-127796000	Bivalent Enhancer	K562	blood
18	chr7:127795600-127796000	Enhancers	Fetal Kidney	kidney
19	chr7:127795600-127797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:127795800-127800400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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