Variant report

Variant	rs66845903
Chromosome Location	chr3:110765841-110765842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-553A10.1.1-1	chr3:110765749-110765878	ENSG00000242242.1

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11919892	1.00[ASN][1000 genomes]
rs11927478	0.80[ASN][1000 genomes]
rs1382075	1.00[ASN][1000 genomes]
rs1462789	0.80[ASN][1000 genomes]
rs1477854	0.99[ASN][1000 genomes]
rs1477855	0.99[ASN][1000 genomes]
rs1585629	0.98[ASN][1000 genomes]
rs1600059	0.99[ASN][1000 genomes]
rs1871026	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2126710	1.00[ASN][1000 genomes]
rs2126711	1.00[ASN][1000 genomes]
rs2126712	1.00[ASN][1000 genomes]
rs28772911	0.89[ASN][1000 genomes]
rs6437940	0.80[ASN][1000 genomes]
rs6765948	0.89[ASN][1000 genomes]
rs6781480	1.00[ASN][1000 genomes]
rs6790828	0.83[ASN][1000 genomes]
rs7632375	1.00[ASN][1000 genomes]
rs7632388	1.00[ASN][1000 genomes]
rs9817950	0.80[ASN][1000 genomes]
rs9818950	1.00[ASN][1000 genomes]
rs9837377	0.98[ASN][1000 genomes]
rs9847598	0.99[ASN][1000 genomes]
rs9877855	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv829674	chr3:110616256-110771049	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110763800-110768600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:110764000-110767400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:110764000-110769000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:110764400-110767200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:110764400-110767400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:110764400-110767800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:110764400-110768800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:110764400-110768800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:110764600-110766200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:110765000-110788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:110765400-110767000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:110765400-110768400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:110765600-110767400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:110765800-110767600	Enhancers	HepG2	liver
15	chr3:110765800-110768000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:110765800-110768600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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