Variant report

Variant	rs1175788
Chromosome Location	chr9:95117798-95117799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10156482	0.85[ASN][1000 genomes]
rs10491806	1.00[YRI][hapmap]
rs10761149	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761152	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10761156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10820950	0.84[EUR][1000 genomes]
rs10820951	0.82[EUR][1000 genomes]
rs10820952	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152757	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1152759	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12552866	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1760318	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs1923599	0.92[CEU][hapmap]
rs1960094	0.83[ASN][1000 genomes]
rs2025389	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2131919	1.00[YRI][hapmap]
rs2147060	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2181712	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs230222	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2398751	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3174352	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs331377	0.92[CEU][hapmap]
rs331379	0.92[CEU][hapmap]
rs331380	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs331381	0.92[CEU][hapmap]
rs3736835	0.89[CEU][hapmap]
rs3780346	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs3996311	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471478	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743869	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744122	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4744126	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504708	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6479417	1.00[YRI][hapmap]
rs6651532	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7028854	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.81[ASN][1000 genomes]
rs7040860	0.81[EUR][1000 genomes]
rs710163	0.88[CEU][hapmap]
rs7467899	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867300	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs9299402	0.82[EUR][1000 genomes]
rs9409664	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409667	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	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
5	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1175788	CENPP	cis	parietal	SCAN
rs1175788	FBP1	cis	parietal	SCAN
rs1175788	CENPP	cis	cerebellum	SCAN
rs1175788	FANCC	cis	cerebellum	SCAN
rs1175788	SPTLC1	cis	parietal	SCAN
rs1175788	OGN	cis	Nerve Tibial	GTEx
rs1175788	ZNF484	cis	cerebellum	SCAN
rs1175788	ZNF484	cis	parietal	SCAN
rs1175788	ECM2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95089600-95121800	Weak transcription	Fetal Heart	heart
2	chr9:95090400-95118200	Weak transcription	HepG2	liver
3	chr9:95091000-95120000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:95102000-95121000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:95102200-95121400	Weak transcription	A549	lung
6	chr9:95102600-95120800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:95104200-95118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:95104200-95119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:95104200-95121200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:95113400-95119400	Weak transcription	Fetal Lung	lung
11	chr9:95113400-95121800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:95113600-95117800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:95116000-95118000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr9:95116400-95118000	Weak transcription	Fetal Thymus	thymus
15	chr9:95116400-95118800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:95116600-95120000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:95116800-95117800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:95116800-95119800	Weak transcription	Lung	lung
19	chr9:95116800-95119800	Weak transcription	Thymus	Thymus
20	chr9:95116800-95122200	Weak transcription	Primary T cells from cord blood	blood
21	chr9:95116800-95127600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:95116800-95128600	Weak transcription	Dnd41	blood
23	chr9:95117000-95118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:95117000-95121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:95117000-95134800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links