Variant report

Variant	rs10877028
Chromosome Location	chr12:58241028-58241029
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10444569	0.88[AMR][1000 genomes]
rs10747784	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747786	0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs10747787	0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs10783850	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783851	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783853	0.81[TSI][hapmap]
rs10783854	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783855	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783856	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877022	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10877024	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877025	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877026	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877029	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10877030	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10877031	0.88[AMR][1000 genomes]
rs10877032	0.86[AMR][1000 genomes]
rs11172361	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172362	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172367	0.84[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs11172368	0.84[AMR][1000 genomes]
rs11172369	0.87[JPT][hapmap];0.83[AMR][1000 genomes]
rs11172371	0.81[AMR][1000 genomes]
rs12312955	0.84[AMR][1000 genomes]
rs12319233	0.84[AMR][1000 genomes]
rs12426201	0.88[AMR][1000 genomes]
rs1599750	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599751	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599931	0.93[JPT][hapmap];0.86[AMR][1000 genomes]
rs1875125	0.85[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1962047	0.80[CHD][hapmap]
rs2002275	0.80[CHD][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs4237844	0.84[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs4237845	0.80[CHD][hapmap]
rs4760171	0.81[ASW][hapmap];0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760172	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4760332	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760333	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760335	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760339	0.83[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes]
rs4760340	0.84[CHD][hapmap]
rs4760341	0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs5017863	0.86[AMR][1000 genomes]
rs59401446	0.86[AMR][1000 genomes]
rs7134797	0.81[AMR][1000 genomes]
rs7298479	0.85[EUR][1000 genomes]
rs7312623	0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs7489290	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954957	0.80[CHD][hapmap]
rs7969844	0.82[AMR][1000 genomes]
rs870392	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs871871	0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9645819	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases
2	nsv826388	chr12:58238659-58242397	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
3	esv3415743	chr12:58239635-58241833	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	n/a

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs10877028	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs10877028	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877028	CDK2	cis	parietal	SCAN
rs10877028	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10877028	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877028	XRCC6BP1	cis	Whole Blood	GTEx
rs10877028	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10877028	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877028	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877028	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877028	STAT6	cis	cerebellum	SCAN
rs10877028	FAM119B	cis	lymphoblastoid	seeQTL
rs10877028	GPR84	cis	cerebellum	SCAN
rs10877028	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877028	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877028	TSFM	cis	lymphoblastoid	seeQTL
rs10877028	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10877028	METTL21B	cis	Muscle Skeletal	GTEx
rs10877028	FAM119B	cis	Frontal Cortex	GTEx
rs10877028	TSPAN31	cis	parietal	SCAN
rs10877028	FAM119B	cis	cerebellum	SCAN
rs10877028	FAM119B	cis	parietal	SCAN
rs10877028	PPP1R1A	cis	parietal	SCAN
rs10877028	TSPAN31	cis	cerebellum	SCAN
rs10877028	FAM119B	cis	Cerebellum	GTEx
rs10877028	FAM119B	cis	Temporal Cortex	GTEx
rs10877028	XRCC6BP1	cis	lung	GTEx
rs10877028	MUCL1	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58237200-58241200	Active TSS	Ovary	ovary
2	chr12:58237400-58241200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:58237600-58241400	Active TSS	Brain Substantia Nigra	brain
4	chr12:58237600-58241400	Active TSS	Fetal Kidney	kidney
5	chr12:58237800-58241200	Active TSS	Colon Smooth Muscle	Colon
6	chr12:58238000-58241200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:58238400-58241200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:58238400-58241200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:58238400-58241200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr12:58238400-58241200	Active TSS	Left Ventricle	heart
11	chr12:58238400-58241200	Active TSS	NHDF-Ad	bronchial
12	chr12:58238400-58241400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:58238400-58241600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr12:58238400-58241800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:58238600-58241200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr12:58238600-58241200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:58238600-58241200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:58238600-58241200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:58238600-58241200	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr12:58238600-58241200	Active TSS	Psoas Muscle	Psoas
21	chr12:58238600-58241200	Active TSS	Right Atrium	heart
22	chr12:58238600-58241400	Active TSS	Brain Hippocampus Middle	brain
23	chr12:58238800-58241200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:58238800-58241200	Active TSS	A549	lung
25	chr12:58238800-58241200	Active TSS	GM12878-XiMat	blood
26	chr12:58238800-58241800	Active TSS	NHEK	skin
27	chr12:58240200-58241200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:58240200-58241200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:58240200-58241200	Active TSS	Fetal Brain Female	brain
30	chr12:58240200-58241400	Active TSS	Brain Germinal Matrix	brain
31	chr12:58240200-58241800	Active TSS	Colonic Mucosa	Colon
32	chr12:58240400-58241200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:58240400-58241200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:58240800-58241200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:58240800-58241200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:58240800-58241200	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr12:58240800-58241200	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr12:58240800-58241200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr12:58240800-58241200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:58240800-58241200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr12:58240800-58241200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:58240800-58241200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:58240800-58241200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr12:58240800-58241200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:58240800-58241200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:58240800-58241200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:58240800-58241200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:58240800-58241200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:58240800-58241200	Flanking Active TSS	Fetal Thymus	thymus
50	chr12:58240800-58241200	Enhancers	Placenta Amnion	Placenta Amnion

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