Variant report

Variant	rs2682053
Chromosome Location	chr15:56544917-56544918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56533157..56539020-chr15:56544541..56548879,7	K562	blood:

Variant related genes	Relation type
ENSG00000151575	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11629483	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630363	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs11631191	0.87[EUR][1000 genomes]
rs11855094	0.94[CHB][hapmap]
rs12900678	1.00[CHB][hapmap]
rs12905782	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12905899	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12914640	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1372753	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1549452	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs16976890	0.94[CHB][hapmap]
rs17819438	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1829542	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2249090	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2303441	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2414464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2460647	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2460648	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2460650	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465973	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2554287	0.94[CHB][hapmap]
rs2682012	0.84[ASN][1000 genomes]
rs2682044	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682046	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2682049	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682054	0.80[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713923	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713924	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713926	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2713931	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2713933	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713938	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713941	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718915	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2718921	0.94[CHB][hapmap]
rs2718941	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2725854	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2725856	0.81[CHB][hapmap]
rs2725870	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2947020	0.81[ASN][1000 genomes]
rs2947021	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34044869	0.80[AMR][1000 genomes]
rs34144128	0.80[AMR][1000 genomes]
rs35749329	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35972806	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3784552	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs3817406	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4310791	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4310792	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59432349	0.87[EUR][1000 genomes]
rs62044110	0.80[EUR][1000 genomes]
rs62044111	0.80[EUR][1000 genomes]
rs6493856	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs6493858	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7168319	0.80[AMR][1000 genomes]
rs7170307	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7174823	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181235	0.94[CHB][hapmap]
rs7496025	0.80[AMR][1000 genomes]
rs795786	0.82[CHB][hapmap]
rs795791	0.88[CHB][hapmap]
rs795800	0.94[CHB][hapmap]
rs8028353	0.80[AMR][1000 genomes]
rs8029114	0.80[AMR][1000 genomes]
rs9672886	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672928	0.81[AMR][1000 genomes];0.82[EUR][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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2682053	RFX7	cis	Adipose Subcutaneous	GTEx
rs2682053	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56538200-56546600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:56538400-56546000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:56538800-56546400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:56538800-56546600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:56543000-56545200	Enhancers	K562	blood
6	chr15:56543200-56545200	Enhancers	Primary hematopoietic stem cells	blood
7	chr15:56543600-56545600	Enhancers	Fetal Intestine Small	intestine
8	chr15:56543800-56545200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:56544000-56545000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:56544200-56545000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr15:56544200-56545000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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