Variant report

Variant	rs10877012
Chromosome Location	chr12:58162085-58162086
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58162027-58162383	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:58159584-58162095	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57912185..57914600-chr12:58159460..58162214,2	MCF-7	breast:
2	chr12:58112950..58114640-chr12:58160149..58162147,2	K562	blood:

Variant related genes	Relation type
ENSG00000257921	TF binding region
METTL21B	TF binding region
CYP27B1	TF binding region
ENSG00000175197	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431505	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747786	0.83[JPT][hapmap]
rs10747787	0.83[JPT][hapmap]
rs10783847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877011	0.85[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877015	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877018	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172342	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172349	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172350	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap]
rs1599931	0.88[JPT][hapmap]
rs1599932	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap]
rs2014886	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2069506	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2072052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825079	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap]
rs4646536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap]
rs56177740	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs701008	0.81[TSI][hapmap]
rs703842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8181644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9652011	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs10877012	FAM119B	cis	lymphoblastoid	seeQTL
rs10877012	METTL21B	cis	Esophagus Mucosa	GTEx
rs10877012	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877012	TSFM	cis	parietal	SCAN
rs10877012	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs10877012	METTL21B	cis	Whole Blood	GTEx
rs10877012	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877012	XRCC6BP1	cis	Whole Blood	GTEx
rs10877012	TSPAN31	cis	cerebellum	SCAN
rs10877012	FAM119B	cis	parietal	SCAN
rs10877012	METTL21B	cis	Adipose Subcutaneous	GTEx
rs10877012	TSFM	cis	cerebellum	SCAN
rs10877012	HSD17B6	cis	cerebellum	SCAN
rs10877012	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877012	TSPAN31	cis	parietal	SCAN
rs10877012	KRT5	cis	cerebellum	SCAN
rs10877012	RP11-571M6.13	cis	Thyroid	GTEx
rs10877012	ESPL1	cis	parietal	SCAN
rs10877012	FAM119B	cis	cerebellum	SCAN
rs10877012	TSFM	cis	lymphoblastoid	seeQTL
rs10877012	METTL21B	cis	Muscle Skeletal	GTEx
rs10877012	TSFM	cis	multi-tissue	Pritchard
rs10877012	GPR84	cis	cerebellum	SCAN
rs10877012	METTL21B	cis	lung	GTEx
rs10877012	WIBG	cis	cerebellum	SCAN
rs10877012	CYP27B1	cis	Thyroid	GTEx
rs10877012	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs10877012	KIAA0748	cis	cerebellum	SCAN
rs10877012	TSFM	cis	Muscle Skeletal	GTEx
rs10877012	METTL21B	cis	Heart Left Ventricle	GTEx
rs10877012	CDK4	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58154000-58162200	Weak transcription	Dnd41	blood
2	chr12:58157000-58162200	Weak transcription	Hela-S3	cervix
3	chr12:58160400-58162200	Weak transcription	HepG2	liver
4	chr12:58160800-58162200	Weak transcription	Spleen	Spleen
5	chr12:58160800-58163400	Weak transcription	GM12878-XiMat	blood
6	chr12:58160800-58164600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:58160800-58164600	Weak transcription	Right Atrium	heart
8	chr12:58160800-58165200	Weak transcription	Brain Substantia Nigra	brain
9	chr12:58161000-58162200	Weak transcription	Aorta	Aorta
10	chr12:58161000-58162200	Weak transcription	Gastric	stomach
11	chr12:58161000-58162400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:58161000-58162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:58161000-58162600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:58161000-58162600	Weak transcription	Left Ventricle	heart
15	chr12:58161000-58163000	Weak transcription	Ovary	ovary
16	chr12:58161000-58163000	Weak transcription	Psoas Muscle	Psoas
17	chr12:58161000-58164800	Weak transcription	Right Ventricle	heart
18	chr12:58161000-58165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:58161000-58165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:58161000-58165200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:58161200-58162200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:58161200-58162200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:58161200-58162200	Weak transcription	Brain Anterior Caudate	brain
24	chr12:58161200-58162200	Weak transcription	Lung	lung
25	chr12:58161200-58162400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:58161200-58162400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:58161200-58162400	Weak transcription	HSMM	muscle
28	chr12:58161200-58164600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:58161200-58164800	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:58161200-58164800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:58161200-58165000	Weak transcription	NH-A	brain
32	chr12:58161200-58165200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:58161400-58162200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:58161400-58162200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:58161400-58162200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:58161400-58162200	Weak transcription	NHLF	lung
37	chr12:58161400-58162400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:58161400-58162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:58161400-58162600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:58161400-58162800	Weak transcription	Fetal Lung	lung
41	chr12:58161400-58163000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:58161400-58163000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:58161400-58163800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:58161400-58164600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:58161400-58164600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:58161400-58164800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:58161400-58164800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:58161400-58164800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:58161400-58164800	Weak transcription	HUVEC	blood vessel
50	chr12:58161400-58165200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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