Variant report

Variant	rs10875768
Chromosome Location	chr12:48599543-48599544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48597340..48600068-chr12:48604806..48607585,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1021313	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10431526	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10437919	0.94[ASN][1000 genomes]
rs10437920	0.94[ASN][1000 genomes]
rs10467101	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783234	0.85[ASN][1000 genomes]
rs10875762	0.88[ASN][1000 genomes]
rs10875764	0.85[ASN][1000 genomes]
rs10875767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875769	0.90[ASN][1000 genomes]
rs10875770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875772	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875777	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875778	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875779	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875782	0.91[ASN][1000 genomes]
rs10875792	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875793	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168450	0.85[ASN][1000 genomes]
rs11168459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168483	0.91[ASN][1000 genomes]
rs11168487	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168493	0.86[ASN][1000 genomes]
rs11168508	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168510	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168514	0.87[ASN][1000 genomes]
rs11168516	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11558768	0.87[ASN][1000 genomes]
rs12227601	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12300647	0.91[ASN][1000 genomes]
rs12305511	0.90[ASN][1000 genomes]
rs12305647	0.90[ASN][1000 genomes]
rs12317751	0.94[ASN][1000 genomes]
rs12318705	0.91[ASN][1000 genomes]
rs17122812	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012773	0.85[ASN][1000 genomes]
rs2171642	0.91[ASN][1000 genomes]
rs2279464	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2409005	0.88[ASN][1000 genomes]
rs2898065	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2898066	0.89[ASN][1000 genomes]
rs4760622	0.90[ASN][1000 genomes]
rs4760625	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4760695	0.90[ASN][1000 genomes]
rs4760696	0.85[ASN][1000 genomes]
rs4760697	0.84[ASN][1000 genomes]
rs4760699	0.86[ASN][1000 genomes]
rs61940962	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61941003	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61941006	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580659	0.86[ASN][1000 genomes]
rs7135779	0.85[ASN][1000 genomes]
rs716553	0.94[ASN][1000 genomes]
rs7297298	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302466	0.91[ASN][1000 genomes]
rs7303055	0.94[ASN][1000 genomes]
rs7486008	0.94[ASN][1000 genomes]
rs7975956	0.91[ASN][1000 genomes]
rs9634261	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv976031	chr12:48594968-48610975	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv976038	chr12:48596152-48610975	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv518743	chr12:48597507-48600520	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10875768	RP1-228P16.1	cis	Thyroid	GTEx
rs10875768	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875768	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48593200-48600200	Weak transcription	Right Ventricle	heart
3	chr12:48593400-48600800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:48595200-48600400	Weak transcription	Psoas Muscle	Psoas
5	chr12:48595600-48609600	Weak transcription	Placenta	Placenta
6	chr12:48595800-48599600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:48595800-48600800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:48596000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:48596600-48603800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:48597000-48606600	Weak transcription	Left Ventricle	heart
11	chr12:48597000-48606800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:48598000-48599600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr12:48598400-48599600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr12:48598400-48600200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:48598600-48599800	ZNF genes & repeats	Ovary	ovary
16	chr12:48599000-48599600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr12:48599000-48599600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:48599000-48599800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:48599200-48606200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:48599400-48600200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:48599400-48600400	Weak transcription	Brain Cingulate Gyrus	brain

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