Variant report

Variant	rs10875766
Chromosome Location	chr12:48593580-48593581
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48593487..48595723-chr12:48689162..48691231,3	K562	blood:
2	chr12:48590039..48593666-chr12:48742360..48744824,3	K562	blood:
3	chr12:48366898..48369197-chr12:48592697..48594577,2	K562	blood:
4	chr12:48510785..48513717-chr12:48592045..48593630,2	K562	blood:
5	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177875	Chromatin interaction
ENSG00000257735	Chromatin interaction
ENSG00000167528	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1049392	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10747529	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10875733	1.00[JPT][hapmap]
rs10875739	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10875752	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875754	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875759	0.88[ASN][1000 genomes]
rs10875761	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10875765	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	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168424	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168434	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168435	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168438	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168439	0.86[ASN][1000 genomes]
rs11168442	0.91[ASN][1000 genomes]
rs11168443	0.90[ASN][1000 genomes]
rs11168444	0.91[ASN][1000 genomes]
rs11168445	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168446	0.91[ASN][1000 genomes]
rs11168447	0.91[ASN][1000 genomes]
rs11168448	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168453	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168454	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12422355	1.00[JPT][hapmap]
rs17122567	1.00[JPT][hapmap]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs2171643	0.92[ASN][1000 genomes]
rs2261608	0.84[CEU][hapmap]
rs2286020	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.94[JPT][hapmap]
rs3752820	0.83[CEU][hapmap]
rs3825403	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs56097189	0.89[ASN][1000 genomes]
rs59537300	0.90[ASN][1000 genomes]
rs6580658	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs66507954	0.91[ASN][1000 genomes]
rs7132898	0.84[ASN][1000 genomes]
rs7133274	0.91[ASN][1000 genomes]
rs7136243	0.91[ASN][1000 genomes]
rs7136782	0.90[ASN][1000 genomes]
rs7136788	0.90[ASN][1000 genomes]
rs7299704	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7301176	0.87[JPT][hapmap]
rs7302354	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7303677	1.00[JPT][hapmap]
rs73105950	0.91[ASN][1000 genomes]
rs73304926	0.91[ASN][1000 genomes]
rs7484942	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs765260	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7962390	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7962569	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs8181670	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs886589	0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875766	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48591200-48594200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr12:48591400-48593600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:48591400-48594000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr12:48591600-48594000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:48592400-48594000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:48592400-48594800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:48592600-48593800	Active TSS	Right Atrium	heart
8	chr12:48592600-48593800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr12:48592600-48593800	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr12:48592600-48594200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr12:48592600-48594200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:48592600-48594400	Weak transcription	Spleen	Spleen
13	chr12:48592600-48595200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr12:48592800-48593600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr12:48592800-48593600	Enhancers	Colonic Mucosa	Colon
16	chr12:48592800-48593800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:48592800-48593800	Flanking Active TSS	GM12878-XiMat	blood
18	chr12:48592800-48594000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr12:48592800-48594000	Enhancers	Small Intestine	intestine
20	chr12:48592800-48594000	Enhancers	Stomach Mucosa	stomach
21	chr12:48592800-48594200	Enhancers	A549	lung
22	chr12:48592800-48594200	Enhancers	Hela-S3	cervix
23	chr12:48592800-48594600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:48592800-48594600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr12:48592800-48594800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr12:48592800-48595200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:48592800-48596000	Weak transcription	Gastric	stomach
28	chr12:48592800-48596000	Weak transcription	Ovary	ovary
29	chr12:48592800-48600400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:48593000-48593600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:48593000-48593600	Enhancers	NHLF	lung
32	chr12:48593000-48593800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:48593000-48593800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:48593000-48593800	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr12:48593000-48594000	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:48593000-48594000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:48593000-48594000	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr12:48593000-48594000	Flanking Active TSS	Fetal Lung	lung
39	chr12:48593000-48594000	Enhancers	Osteobl	bone
40	chr12:48593000-48594200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:48593000-48594200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr12:48593000-48594400	Weak transcription	Esophagus	oesophagus
43	chr12:48593000-48594400	Enhancers	Fetal Intestine Small	intestine
44	chr12:48593000-48594600	Enhancers	Fetal Intestine Large	intestine
45	chr12:48593000-48595000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:48593000-48595600	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr12:48593000-48595600	Enhancers	Placenta	Placenta
48	chr12:48593000-48596600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:48593200-48593600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:48593200-48593600	Enhancers	Liver	Liver

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