Variant report

Variant	rs10877019
Chromosome Location	chr12:58172929-58172930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58171107..58173355-chr12:58182037..58183713,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 39 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1021469	0.92[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10431505	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783850	1.00[LWK][hapmap]
rs10783851	1.00[LWK][hapmap]
rs10783853	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs10877011	0.85[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs10877012	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]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[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];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877017	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877029	0.83[JPT][hapmap]
rs10877030	0.83[JPT][hapmap]
rs11172333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172342	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172350	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs11172371	0.85[YRI][hapmap]
rs1599931	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs1599932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1689585	0.83[GIH][hapmap]
rs1875124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs2014886	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2069502	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2069506	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782130	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825079	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[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];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760171	0.83[JPT][hapmap]
rs4760172	0.83[JPT][hapmap]
rs4760332	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap]
rs56177740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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[GIH][hapmap];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];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652011	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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:39)

SNP	Gene	Cis/trans	Tissue	Source
rs10877019	TSFM	cis	Muscle Skeletal	GTEx
rs10877019	FAM119B	cis	cerebellum	SCAN
rs10877019	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877019	METTL21B	cis	Esophagus Mucosa	GTEx
rs10877019	FAM119B	cis	brain	seeQTL
rs10877019	FAM119B	cis	multi-tissue	Pritchard
rs10877019	KIAA0748	cis	cerebellum	SCAN
rs10877019	RP11-571M6.13	cis	Thyroid	GTEx
rs10877019	ESPL1	cis	parietal	SCAN
rs10877019	FAM119B	cis	Liver	GTEx
rs10877019	TSPAN31	cis	parietal	SCAN
rs10877019	TSFM	cis	lymphoblastoid	seeQTL
rs10877019	TSPAN31	cis	cerebellum	SCAN
rs10877019	FAM119B	cis	Lymphoblastoid	GTEx
rs10877019	HSD17B6	cis	cerebellum	SCAN
rs10877019	XRCC6BP1	cis	multi-tissue	Pritchard
rs10877019	METTL21B	cis	Whole Blood	GTEx
rs10877019	METTL21B	cis	Esophagus Muscularis	GTEx
rs10877019	KRT5	cis	cerebellum	SCAN
rs10877019	TSFM	cis	Liver	GTEx
rs10877019	FAM119B	cis	Brain Pons	GTEx
rs10877019	CYP27B1	cis	Thyroid	GTEx
rs10877019	METTL21B	cis	Adipose Subcutaneous	GTEx
rs10877019	DKFZP586D0919	cis	multi-tissue	Pritchard
rs10877019	CDK4	cis	cerebellum	SCAN
rs10877019	TSFM	cis	multi-tissue	Pritchard
rs10877019	FAM119B	cis	parietal	SCAN
rs10877019	XRCC6BP1	cis	brain	seeQTL
rs10877019	FAM119B	cis	lymphoblastoid	seeQTL
rs10877019	FAM119B	cis	Cerebellum	GTEx
rs10877019	GPR84	cis	cerebellum	SCAN
rs10877019	METTL21B	cis	Heart Left Ventricle	GTEx
rs10877019	TSFM	cis	cerebellum	SCAN
rs10877019	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs10877019	TSFM	cis	parietal	SCAN
rs10877019	METTL21B	cis	Muscle Skeletal	GTEx
rs10877019	WIBG	cis	cerebellum	SCAN
rs10877019	FAM119B	cis	Frontal Cortex	GTEx
rs10877019	METTL21B	cis	lung	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58166800-58176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:58167000-58173600	Weak transcription	Brain Anterior Caudate	brain
3	chr12:58167000-58173600	Weak transcription	Esophagus	oesophagus
4	chr12:58167000-58174000	Weak transcription	Aorta	Aorta
5	chr12:58167000-58175600	Weak transcription	Spleen	Spleen
6	chr12:58167000-58175800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:58167000-58176400	Weak transcription	Gastric	stomach
8	chr12:58167200-58173600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:58167200-58173800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:58167200-58174000	Weak transcription	Primary T cells from cord blood	blood
11	chr12:58167200-58174000	Weak transcription	Brain Germinal Matrix	brain
12	chr12:58167200-58174000	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:58167200-58174200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:58167200-58174200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:58167200-58174400	Weak transcription	Liver	Liver
16	chr12:58167200-58174600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:58167200-58175600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:58167200-58176000	Weak transcription	Brain Angular Gyrus	brain
19	chr12:58167200-58176000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:58167200-58176400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:58167200-58176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:58167200-58176400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:58167200-58176400	Weak transcription	Right Ventricle	heart
24	chr12:58167400-58175600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:58167400-58175600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:58167400-58176000	Weak transcription	Fetal Intestine Large	intestine
27	chr12:58167400-58176200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:58167400-58176200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:58167400-58176400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:58167400-58176400	Weak transcription	Colonic Mucosa	Colon
31	chr12:58167400-58176400	Weak transcription	Left Ventricle	heart
32	chr12:58167600-58173400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:58167600-58173600	Weak transcription	Pancreas	Pancrea
34	chr12:58167600-58174000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:58167600-58174000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:58167600-58174200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:58167600-58175800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:58167600-58175800	Weak transcription	HepG2	liver
39	chr12:58167600-58175800	Weak transcription	K562	blood
40	chr12:58167600-58176000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:58167600-58176000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:58167600-58176000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:58167600-58176200	Weak transcription	NH-A	brain
44	chr12:58167600-58176200	Weak transcription	NHDF-Ad	bronchial
45	chr12:58167600-58176400	Weak transcription	Placenta	Placenta
46	chr12:58167600-58176400	Weak transcription	HSMMtube	muscle
47	chr12:58167600-58176600	Weak transcription	Fetal Brain Male	brain
48	chr12:58167800-58173000	Weak transcription	Adipose Nuclei	Adipose
49	chr12:58167800-58173600	Weak transcription	Dnd41	blood
50	chr12:58167800-58173600	Weak transcription	Osteobl	bone

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