Variant report

Variant	rs2682051
Chromosome Location	chr15:56543422-56543423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56541414..56543622-chr15:56724476..56727386,2	K562	blood:
2	chr15:56536983..56539715-chr15:56539921..56543667,5	K562	blood:
3	chr15:56494171..56496972-chr15:56541763..56543619,2	K562	blood:

Variant related genes	Relation type
ENSG00000138587	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11629483	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630363	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11631191	0.87[EUR][1000 genomes]
rs11855094	0.91[CHB][hapmap]
rs12900678	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap]
rs12905782	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap]
rs12905899	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911094	0.92[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs12911427	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs12914640	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1372753	0.92[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1402177	0.81[AMR][1000 genomes]
rs1549452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs16976890	0.91[CHB][hapmap]
rs17819438	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs1829542	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2119937	0.92[CEU][hapmap]
rs2249090	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2303441	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2414464	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2460647	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2460648	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2460650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465973	0.84[AMR][1000 genomes]
rs2554287	0.91[CHB][hapmap]
rs2682012	0.82[ASN][1000 genomes]
rs2682019	0.81[AMR][1000 genomes]
rs2682044	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2682046	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682049	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682053	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	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682059	1.00[CEU][hapmap]
rs2713923	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713926	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2713931	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2713933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713935	0.81[CEU][hapmap]
rs2713936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713938	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713941	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718915	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2718921	0.91[CHB][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2725856	0.82[CHB][hapmap]
rs2725870	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2947020	0.83[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34044869	0.82[AMR][1000 genomes]
rs34144128	0.82[AMR][1000 genomes]
rs35749329	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35972806	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3784552	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3817406	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4310791	1.00[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4774232	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs4774847	0.80[EUR][1000 genomes]
rs59432349	0.87[EUR][1000 genomes]
rs62044110	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62044111	0.81[EUR][1000 genomes]
rs6493856	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs6493858	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs7168319	0.82[AMR][1000 genomes]
rs7170307	0.89[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap]
rs7174823	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap]
rs7181235	0.91[CHB][hapmap]
rs7496025	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs795790	0.82[CEU][hapmap]
rs795791	0.86[CHB][hapmap]
rs795800	0.91[CHB][hapmap]
rs8024031	0.92[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs8028353	0.82[AMR][1000 genomes]
rs8029114	0.82[AMR][1000 genomes]
rs9672886	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9672928	0.83[AMR][1000 genomes];0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2682051	RFX7	cis	Adipose Subcutaneous	GTEx
rs2682051	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2682051	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 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	chr15:56538400-56544000	Weak transcription	Fetal Brain Male	brain
3	chr15:56538400-56546000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:56538800-56544000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:56538800-56544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:56538800-56546400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:56538800-56546600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:56540800-56544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:56541200-56543800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:56541400-56543800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:56541400-56543800	Weak transcription	Stomach Mucosa	stomach
12	chr15:56541400-56544200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:56541600-56544000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:56542400-56543600	Weak transcription	Fetal Intestine Small	intestine
15	chr15:56543000-56545200	Enhancers	K562	blood
16	chr15:56543200-56545200	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:56543400-56544400	Enhancers	Skeletal Muscle Female	skeletal muscle

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