Variant report

Variant	rs10875754
Chromosome Location	chr12:48557922-48557923
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48500571..48503072-chr12:48556879..48559027,2	K562	blood:
2	chr12:48549808..48555740-chr12:48556420..48560606,6	K562	blood:
3	chr12:48239241..48242168-chr12:48557559..48560161,2	K562	blood:

Variant related genes	Relation type
ENSG00000258051	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1049392	1.00[JPT][hapmap]
rs10747529	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10875733	1.00[JPT][hapmap]
rs10875739	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10875741	0.80[ASN][1000 genomes]
rs10875744	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875752	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875759	0.91[ASN][1000 genomes]
rs10875761	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875765	0.86[ASN][1000 genomes]
rs10875766	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	1.00[JPT][hapmap]
rs11168364	1.00[JPT][hapmap]
rs11168373	1.00[JPT][hapmap]
rs11168404	1.00[JPT][hapmap]
rs11168417	1.00[JPT][hapmap]
rs11168424	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11168434	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168435	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168438	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168439	0.92[ASN][1000 genomes]
rs11168442	0.85[ASN][1000 genomes]
rs11168443	0.86[ASN][1000 genomes]
rs11168444	0.85[ASN][1000 genomes]
rs11168445	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168446	0.85[ASN][1000 genomes]
rs11168447	0.85[ASN][1000 genomes]
rs11168448	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168453	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168454	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12422355	1.00[JPT][hapmap]
rs12423250	0.94[JPT][hapmap]
rs12425679	0.81[ASN][1000 genomes]
rs17122567	1.00[JPT][hapmap]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.82[JPT][hapmap]
rs2158515	0.89[CEU][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171643	0.86[ASN][1000 genomes]
rs2286020	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.94[JPT][hapmap]
rs3825403	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4258439	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs56097189	0.90[ASN][1000 genomes]
rs57430775	0.81[ASN][1000 genomes]
rs58556309	0.81[ASN][1000 genomes]
rs59537300	0.86[ASN][1000 genomes]
rs6580658	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs66507954	0.85[ASN][1000 genomes]
rs7132898	0.94[ASN][1000 genomes]
rs7133274	0.85[ASN][1000 genomes]
rs7136243	0.85[ASN][1000 genomes]
rs7136782	0.86[ASN][1000 genomes]
rs7136788	0.84[ASN][1000 genomes]
rs7138917	0.83[CEU][hapmap]
rs7299704	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7302354	1.00[JPT][hapmap]
rs7303677	1.00[JPT][hapmap]
rs7304428	0.80[ASN][1000 genomes]
rs73105950	0.85[ASN][1000 genomes]
rs73304926	0.85[ASN][1000 genomes]
rs7484942	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs765260	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7962390	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7962569	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs8181670	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs886589	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs954326	0.94[JPT][hapmap]
rs9651981	0.94[JPT][hapmap]
rs9804751	0.94[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10875754	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875754	RP1-228P16.1	cis	Thyroid	GTEx
rs10875754	ZNF641	cis	Whole Blood	GTEx
rs10875754	RP1-228P16.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48554800-48558200	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:48555000-48558200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:48557000-48559200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:48557200-48558400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr12:48557200-48559000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:48557400-48559000	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr12:48557800-48558000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48557800-48558800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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