Variant report

Variant	rs11172335
Chromosome Location	chr12:58175201-58175202
allele	C/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	CEBPB	chr12:58175079-58175378	A549	lung:	n/a	n/a
2	CEBPB	chr12:58175105-58175326	K562	blood:	n/a	n/a
3	CEBPB	chr12:58175101-58175364	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:58175076-58175319	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58174276..58176764-chr12:58197954..58200651,2	K562	blood:
2	chr12:58175049..58178042-chr12:58240093..58242141,3	K562	blood:

Variant related genes	Relation type
TSFM	TF binding region
ENSG00000135407	Chromatin interaction
ENSG00000206749	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 35 )

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];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10431505	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783850	1.00[LWK][hapmap]
rs10783851	1.00[LWK][hapmap]
rs10783853	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10877011	0.85[CEU][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];1.00[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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877013	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.85[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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877019	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]
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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172342	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172350	0.97[EUR][1000 genomes];0.85[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];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172367	0.83[JPT][hapmap]
rs11172369	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11172371	1.00[YRI][hapmap]
rs1599931	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1599932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875125	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2014886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2069506	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291617	1.00[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237844	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs4646536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[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];0.85[YRI][hapmap]
rs4760339	0.82[JPT][hapmap]
rs4760341	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs56177740	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312623	0.83[JPT][hapmap]
rs7965287	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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870392	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs871871	0.88[JPT][hapmap]
rs923829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652011	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:35)

SNP	Gene	Cis/trans	Tissue	Source
rs11172335	GPR84	cis	cerebellum	SCAN
rs11172335	HSD17B6	cis	cerebellum	SCAN
rs11172335	FAM119B	cis	Frontal Cortex	GTEx
rs11172335	TSFM	cis	cerebellum	SCAN
rs11172335	KRT5	cis	cerebellum	SCAN
rs11172335	FAM119B	cis	lymphoblastoid	seeQTL
rs11172335	TSPAN31	cis	parietal	SCAN
rs11172335	METTL21B	cis	Muscle Skeletal	GTEx
rs11172335	METTL21B	cis	Heart Left Ventricle	GTEx
rs11172335	KIAA0748	cis	cerebellum	SCAN
rs11172335	TSFM	cis	Muscle Skeletal	GTEx
rs11172335	CDK4	cis	cerebellum	SCAN
rs11172335	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs11172335	METTL21B	cis	Esophagus Mucosa	GTEx
rs11172335	METTL21B	cis	lung	GTEx
rs11172335	FAM119B	cis	parietal	SCAN
rs11172335	FAM119B	cis	Brain Pons	GTEx
rs11172335	TSFM	cis	multi-tissue	Pritchard
rs11172335	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs11172335	METTL21B	cis	Whole Blood	GTEx
rs11172335	TSFM	cis	lymphoblastoid	seeQTL
rs11172335	TSPAN31	cis	cerebellum	SCAN
rs11172335	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172335	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs11172335	METTL21B	cis	Esophagus Muscularis	GTEx
rs11172335	FAM119B	cis	Cerebellum	GTEx
rs11172335	WIBG	cis	cerebellum	SCAN
rs11172335	FAM119B	cis	Lymphoblastoid	GTEx
rs11172335	RP11-571M6.13	cis	Thyroid	GTEx
rs11172335	TSFM	cis	parietal	SCAN
rs11172335	FAM119B	cis	cerebellum	SCAN
rs11172335	METTL21B	cis	Adipose Subcutaneous	GTEx
rs11172335	CYP27B1	cis	Thyroid	GTEx
rs11172335	DKFZP586D0919	cis	multi-tissue	Pritchard
rs11172335	ESPL1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58166800-58176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:58167000-58175600	Weak transcription	Spleen	Spleen
3	chr12:58167000-58175800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:58167000-58176400	Weak transcription	Gastric	stomach
5	chr12:58167200-58175600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:58167200-58176000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:58167200-58176000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:58167200-58176400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:58167200-58176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:58167200-58176400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:58167200-58176400	Weak transcription	Right Ventricle	heart
12	chr12:58167400-58175600	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:58167400-58175600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:58167400-58176000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:58167400-58176200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:58167400-58176200	Weak transcription	Brain Substantia Nigra	brain
17	chr12:58167400-58176400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:58167400-58176400	Weak transcription	Colonic Mucosa	Colon
19	chr12:58167400-58176400	Weak transcription	Left Ventricle	heart
20	chr12:58167600-58175800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:58167600-58175800	Weak transcription	HepG2	liver
22	chr12:58167600-58175800	Weak transcription	K562	blood
23	chr12:58167600-58176000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:58167600-58176000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:58167600-58176000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:58167600-58176200	Weak transcription	NH-A	brain
27	chr12:58167600-58176200	Weak transcription	NHDF-Ad	bronchial
28	chr12:58167600-58176400	Weak transcription	Placenta	Placenta
29	chr12:58167600-58176400	Weak transcription	HSMMtube	muscle
30	chr12:58167600-58176600	Weak transcription	Fetal Brain Male	brain
31	chr12:58167800-58176000	Weak transcription	HMEC	breast
32	chr12:58167800-58176200	Weak transcription	Fetal Kidney	kidney
33	chr12:58167800-58176400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:58168600-58176000	Weak transcription	Hela-S3	cervix
35	chr12:58169400-58175400	Strong transcription	Fetal Muscle Leg	muscle
36	chr12:58170000-58175600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:58170000-58175800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:58170000-58176200	Weak transcription	A549	lung
39	chr12:58170000-58176400	Weak transcription	HSMM	muscle
40	chr12:58170200-58176400	Weak transcription	Ovary	ovary
41	chr12:58170400-58176400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:58170400-58176400	Weak transcription	NHLF	lung
43	chr12:58171400-58176200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:58171600-58176400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:58172000-58175400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:58172000-58176200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr12:58172400-58176200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:58173600-58175400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr12:58173600-58175400	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:58173600-58175400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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