Variant report

Variant	rs2075472
Chromosome Location	chr19:36602097-36602098
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	POLR2A	chr19:36596983-36603152	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:36601329-36602725	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:36601957-36602546	K562	blood:	n/a	n/a
4	POLR2A	chr19:36601321-36602412	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:36602021-36602467	A549	lung:	n/a	n/a
6	SIN3A	chr19:36601722-36602402	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:36602025-36602169	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36601521..36604291-chr19:36630338..36633807,8	MCF-7	breast:
2	chr19:36601583..36604210-chr19:36609754..36611847,2	MCF-7	breast:

Variant related genes	Relation type
TBCB	TF binding region
OVOL3	TF binding region
ENSG00000105254	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1009381	0.93[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10406862	0.93[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10418079	0.81[ASN][1000 genomes]
rs10419924	0.93[ASN][1000 genomes]
rs10420345	0.85[ASN][1000 genomes]
rs10422055	0.93[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10425700	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10427033	0.95[ASN][1000 genomes]
rs11538454	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669405	1.00[LWK][hapmap]
rs11669890	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462159	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12608517	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12981698	0.93[CHB][hapmap];0.83[CHD][hapmap]
rs17884776	1.00[LWK][hapmap]
rs2023866	0.84[ASN][1000 genomes]
rs2074435	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141959	0.89[ASN][1000 genomes]
rs2227260	0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2231568	0.84[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2301734	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2301737	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2871649	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4555271	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4806249	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4806254	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4806262	0.85[ASN][1000 genomes]
rs4806271	0.92[ASN][1000 genomes]
rs4806273	0.89[ASN][1000 genomes]
rs4806276	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55849299	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250364	0.98[ASN][1000 genomes]
rs7251912	0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7258807	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs73036134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8112640	0.89[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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS 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 target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2075472	CYP2A7	cis	parietal	SCAN
rs2075472	CYP2A7	cis	cerebellum	SCAN
rs2075472	ZNF420	cis	cerebellum	SCAN
rs2075472	LOC390940	cis	parietal	SCAN
rs2075472	PHLDB3	cis	parietal	SCAN
rs2075472	ZNF527	cis	cerebellum	SCAN
rs2075472	PHLDB3	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
2	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:36573800-36602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:36574600-36604400	Weak transcription	NHDF-Ad	bronchial
6	chr19:36575400-36604200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:36585000-36602400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:36585200-36604400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:36588400-36604800	Weak transcription	NH-A	brain
10	chr19:36590200-36604600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:36590400-36605000	Weak transcription	Aorta	Aorta
12	chr19:36590600-36604800	Weak transcription	Psoas Muscle	Psoas
13	chr19:36592200-36602400	Weak transcription	Brain Substantia Nigra	brain
14	chr19:36592400-36604800	Weak transcription	Right Atrium	heart
15	chr19:36593200-36602600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:36593400-36603400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:36594000-36602400	Weak transcription	Fetal Lung	lung
18	chr19:36594000-36603400	Weak transcription	Hela-S3	cervix
19	chr19:36594200-36602400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:36594800-36603600	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:36594800-36604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:36595000-36602600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:36595000-36603600	Weak transcription	HepG2	liver
24	chr19:36595600-36603400	Weak transcription	Brain Angular Gyrus	brain
25	chr19:36595600-36603400	Weak transcription	HSMM	muscle
26	chr19:36595600-36603400	Weak transcription	HUVEC	blood vessel
27	chr19:36595600-36604000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:36595800-36604000	Weak transcription	HMEC	breast
29	chr19:36596200-36603400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:36596200-36603800	Weak transcription	GM12878-XiMat	blood
31	chr19:36596200-36604000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:36596400-36603600	Weak transcription	Osteobl	bone
33	chr19:36596600-36603400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:36596600-36603800	Weak transcription	K562	blood
35	chr19:36597600-36602800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:36597600-36603400	Weak transcription	Right Ventricle	heart
37	chr19:36597600-36603400	Weak transcription	Dnd41	blood
38	chr19:36597600-36604600	Weak transcription	HSMMtube	muscle
39	chr19:36597800-36602200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr19:36598000-36603400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr19:36598200-36603600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:36598200-36604000	Weak transcription	Fetal Brain Male	brain
43	chr19:36598400-36602200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr19:36598400-36602400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:36599400-36603800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:36599800-36602200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:36600200-36603800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:36600200-36604400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:36600800-36604400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr19:36601000-36604000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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