Variant report

Variant	rs10875753
Chromosome Location	chr12:48557141-48557142
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	chr12:48500571..48503072-chr12:48556879..48559027,2	K562	blood:
2	chr12:48549808..48555740-chr12:48556420..48560606,6	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10875716	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs10875718	0.80[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs10875719	0.80[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs10875743	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs10875749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875763	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1107654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs11168351	0.81[CEU][hapmap]
rs11168408	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs11168428	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11168437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11168441	1.00[CHB][hapmap];0.88[AMR][1000 genomes]
rs11168460	1.00[CHB][hapmap]
rs12228750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12368659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12816820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17122498	1.00[CHB][hapmap]
rs2051851	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2054905	1.00[CHB][hapmap]
rs2408955	0.86[GIH][hapmap]
rs2450994	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2634681	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2634684	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2732448	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2732466	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2732481	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs2732484	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs3087716	0.85[AMR][1000 genomes]
rs3997	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs4760612	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4760679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs6580650	0.92[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs6580654	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7139330	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7297824	1.00[CHB][hapmap]
rs7301003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7307566	1.00[CHB][hapmap]
rs7315820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs7486941	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs7487682	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs7971880	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs7975632	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs8716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs923397	1.00[CHD][hapmap];0.83[GIH][hapmap]
rs973398	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs9971924	0.84[EUR][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10875753	PRPF40B	cis	parietal	SCAN
rs10875753	C12orf68	cis	cerebellum	SCAN
rs10875753	SENP1	cis	parietal	SCAN
rs10875753	OR6C70	trans	parietal	SCAN
rs10875753	RPAP3	cis	cerebellum	SCAN
rs10875753	H1FNT	cis	Muscle Skeletal	GTEx
rs10875753	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875753	DDX23	cis	parietal	SCAN
rs10875753	PFKM	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:48554800-48558200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:48555000-48558200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:48555600-48557200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:48556000-48557200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:48556000-48557200	Weak transcription	K562	blood
7	chr12:48556600-48557200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr12:48556600-48557400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:48556800-48557200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:48556800-48557400	Enhancers	Brain Anterior Caudate	brain
11	chr12:48557000-48557200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr12:48557000-48557400	Enhancers	Psoas Muscle	Psoas
13	chr12:48557000-48557800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:48557000-48559200	Enhancers	Cortex derived primary cultured neurospheres	brain

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