Variant report

Variant	rs772475
Chromosome Location	chr12:56277498-56277499
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	chr12:56276249..56278200-chr12:56283079..56285139,3	K562	blood:
2	chr12:56222854..56224376-chr12:56275059..56277720,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135392	Chromatin interaction
ENSG00000182796	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10128982	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052206	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs10783775	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes]
rs10876858	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876861	0.87[ASN][1000 genomes]
rs10876862	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.80[ASN][1000 genomes]
rs11171688	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1136082	0.93[AFR][1000 genomes]
rs12298127	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320309	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12817350	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12824144	1.00[YRI][hapmap]
rs12827688	1.00[YRI][hapmap]
rs1463592	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1681070	0.83[AMR][1000 genomes]
rs1681082	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1701698	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1701699	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2101718	0.93[AFR][1000 genomes]
rs4414258	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6581086	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581087	0.84[AMR][1000 genomes]
rs705711	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs705715	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7068	1.00[YRI][hapmap]
rs7135133	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297871	0.89[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs7302957	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7308505	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs772461	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs772468	0.81[AMR][1000 genomes]
rs772700	0.86[ASW][hapmap];0.83[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs772704	0.82[CEU][hapmap]
rs7979046	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739192	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9739196	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv719	chr12:56246405-56290812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
3	esv3347258	chr12:56267734-56298106	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs772475	SDR9C7	cis	cerebellum	SCAN
rs772475	LARP4	cis	parietal	SCAN
rs772475	ATP5G2	cis	parietal	SCAN
rs772475	GLS2	cis	cerebellum	SCAN
rs772475	WIBG	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56270600-56292600	Weak transcription	HSMMtube	muscle
2	chr12:56273800-56292600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:56275400-56277600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56275400-56279200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:56277000-56292600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:56277400-56277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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