Variant report

Variant	rs7246292
Chromosome Location	chr19:36572564-36572565
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	chr19:36565855..36568123-chr19:36571132..36573817,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1003470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420353	0.85[YRI][hapmap]
rs10421966	0.91[YRI][hapmap]
rs10853945	0.97[ASN][1000 genomes]
rs12462674	0.87[YRI][hapmap]
rs12980591	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12982375	0.96[ASN][1000 genomes]
rs1548505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548506	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1972511	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985404	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2023865	0.87[YRI][hapmap]
rs2051800	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2072605	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2239510	0.82[YRI][hapmap]
rs2285745	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2301736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2311004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746271	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826995	0.87[YRI][hapmap]
rs4461192	0.86[YRI][hapmap]
rs4805160	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806265	0.91[ASN][1000 genomes]
rs4806269	0.96[ASN][1000 genomes]
rs4806270	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6510519	0.87[ASN][1000 genomes]
rs757223	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs8103569	0.87[YRI][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7246292	ATXN7L1	trans	parietal	SCAN
rs7246292	CYP2B7P1	cis	parietal	SCAN
rs7246292	ZNF229	cis	parietal	SCAN
rs7246292	GRIK5	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
4	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
6	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
8	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
12	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
14	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
15	chr19:36558800-36574000	Weak transcription	Gastric	stomach
16	chr19:36559200-36572600	Weak transcription	Fetal Brain Female	brain
17	chr19:36559200-36572800	Weak transcription	Brain Germinal Matrix	brain
18	chr19:36560400-36580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:36561200-36597600	Strong transcription	Dnd41	blood
23	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:36561800-36574200	Weak transcription	NH-A	brain
29	chr19:36562000-36588600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr19:36562200-36585000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:36563000-36572600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:36563000-36594200	Weak transcription	HSMM	muscle
33	chr19:36564400-36574200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:36564800-36584600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:36566000-36592000	Weak transcription	HMEC	breast
36	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:36568800-36574400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:36568800-36594800	Strong transcription	A549	lung
39	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
41	chr19:36570200-36575200	Strong transcription	Hela-S3	cervix
42	chr19:36570200-36585200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:36570800-36573000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:36571200-36583800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:36571600-36574600	Strong transcription	NHDF-Ad	bronchial
46	chr19:36571600-36584600	Strong transcription	Thymus	Thymus
47	chr19:36571600-36586400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:36571600-36596600	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr19:36571800-36572600	Enhancers	Brain Hippocampus Middle	brain
50	chr19:36571800-36573200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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