Variant report

Variant	rs757223
Chromosome Location	chr19:36574798-36574799
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	chr19:36573980..36576951-chr19:36606022..36609140,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105254	Chromatin interaction
ENSG00000105258	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1003470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1009381	0.81[CEU][hapmap]
rs10420345	0.83[EUR][1000 genomes]
rs10422055	0.81[CEU][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10426582	0.85[YRI][hapmap]
rs10853945	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12980591	0.97[ASN][1000 genomes]
rs12982375	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1548505	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1548506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972511	0.99[ASN][1000 genomes]
rs1985404	0.99[ASN][1000 genomes]
rs2051800	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072605	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074435	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2227260	0.81[EUR][1000 genomes]
rs2231568	0.81[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs2285745	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs2301736	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2311004	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3746271	0.98[ASN][1000 genomes]
rs4805154	0.85[YRI][hapmap]
rs4805160	0.98[ASN][1000 genomes]
rs4806262	0.85[EUR][1000 genomes]
rs4806265	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4806269	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806270	0.99[ASN][1000 genomes]
rs4806273	0.84[EUR][1000 genomes]
rs6510519	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7245762	0.88[YRI][hapmap]
rs7246292	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7250448	0.88[YRI][hapmap]
rs7257383	0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs757223	POLR2I	cis	multi-tissue	Pritchard
rs757223	PHLDB3	cis	cerebellum	SCAN
rs757223	PHLDB3	cis	parietal	SCAN
rs757223	PSG9	cis	cerebellum	SCAN
rs757223	CYP2A7	cis	parietal	SCAN

Chromatin state (count:95 , 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	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
6	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
10	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
12	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
13	chr19:36560400-36580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:36561200-36597600	Strong transcription	Dnd41	blood
18	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr19:36562000-36588600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr19:36562200-36585000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:36563000-36594200	Weak transcription	HSMM	muscle
26	chr19:36564800-36584600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:36566000-36592000	Weak transcription	HMEC	breast
28	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:36568800-36594800	Strong transcription	A549	lung
30	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
32	chr19:36570200-36575200	Strong transcription	Hela-S3	cervix
33	chr19:36570200-36585200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:36571200-36583800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr19:36571600-36584600	Strong transcription	Thymus	Thymus
36	chr19:36571600-36586400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:36571600-36596600	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr19:36571800-36575200	Strong transcription	K562	blood
39	chr19:36571800-36575800	Strong transcription	HepG2	liver
40	chr19:36571800-36588400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:36571800-36588600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:36571800-36591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:36571800-36598400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
46	chr19:36572000-36575200	Strong transcription	GM12878-XiMat	blood
47	chr19:36572000-36578000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:36572000-36598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:36572200-36575200	Strong transcription	Fetal Intestine Large	intestine
50	chr19:36572200-36575800	Strong transcription	NHLF	lung

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