Variant report

Variant	rs2147060
Chromosome Location	chr9:95160477-95160478
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	chr9:95155268..95158925-chr9:95160273..95163246,4	K562	blood:

Variant related genes	Relation type
ENSG00000106809	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10761149	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs10761156	1.00[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs10820952	0.96[CEU][hapmap]
rs1152757	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs1152759	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1175788	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1760318	0.93[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap]
rs1923599	0.93[CEU][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2025389	1.00[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2031262	1.00[CEU][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2181712	0.82[EUR][1000 genomes]
rs230222	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2398751	0.86[EUR][1000 genomes]
rs3174352	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs331377	0.89[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap]
rs331379	0.89[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap]
rs331380	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs331381	0.89[ASW][hapmap];0.93[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap]
rs3736835	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs3780346	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs3996311	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs471478	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4743869	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs4744126	0.81[EUR][1000 genomes]
rs504708	0.81[EUR][1000 genomes]
rs6651532	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap]
rs7040860	0.84[EUR][1000 genomes]
rs710163	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7467899	0.87[EUR][1000 genomes]
rs7867300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299402	0.88[EUR][1000 genomes]
rs9409664	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs9409667	0.81[EUR][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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1053205	chr9:95119195-95182612	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2147060	CENPP	cis	parietal	SCAN
rs2147060	IPPK	cis	cerebellum	SCAN
rs2147060	FBP1	cis	parietal	SCAN
rs2147060	ZNF484	cis	parietal	SCAN
rs2147060	ECM2	cis	cerebellum	SCAN
rs2147060	CENPP	cis	cerebellum	SCAN
rs2147060	FANCC	cis	cerebellum	SCAN
rs2147060	ZNF484	cis	cerebellum	SCAN
rs2147060	SPTLC1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95139000-95163200	Weak transcription	Aorta	Aorta
2	chr9:95142200-95165600	Weak transcription	Fetal Thymus	thymus
3	chr9:95145000-95163800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:95148000-95164000	Weak transcription	Adipose Nuclei	Adipose
5	chr9:95148400-95163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:95155600-95166600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:95156200-95168200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:95156400-95164200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:95156800-95164000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:95158800-95161600	Strong transcription	Fetal Muscle Leg	muscle
11	chr9:95159200-95160800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:95159800-95163800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:95159800-95164000	Weak transcription	Fetal Intestine Large	intestine
14	chr9:95159800-95165600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:95160000-95160600	ZNF genes & repeats	Fetal Lung	lung
16	chr9:95160000-95163800	Weak transcription	Fetal Intestine Small	intestine
17	chr9:95160000-95166400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:95160200-95160800	Weak transcription	Fetal Stomach	stomach
19	chr9:95160200-95166600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:95160400-95163800	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:95160400-95163800	Weak transcription	Ovary	ovary

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