Variant report

Variant	rs11669890
Chromosome Location	chr19:36564653-36564654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36563782..36565540-chr19:36630314..36632350,2	MCF-7	breast:
2	chr19:36562817..36565517-chr19:36604605..36606772,2	MCF-7	breast:
3	chr19:36543772..36546988-chr19:36561665..36565427,3	MCF-7	breast:
4	chr19:36562998..36565193-chr19:36602097..36603847,2	MCF-7	breast:
5	chr19:36564403..36567348-chr19:36606272..36608349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161277	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1009381	0.92[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs10406862	0.92[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10419924	0.85[ASN][1000 genomes]
rs10420345	0.88[ASN][1000 genomes]
rs10421377	0.82[ASN][1000 genomes]
rs10422055	0.92[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs10425700	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10427033	0.88[ASN][1000 genomes]
rs11538454	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666192	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462159	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12608517	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12981698	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs2023866	0.87[ASN][1000 genomes]
rs2074435	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2075472	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]
rs2141959	0.85[ASN][1000 genomes]
rs2227260	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs2231568	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs2301734	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2301737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2871649	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4555271	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4806249	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4806254	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4806262	0.88[ASN][1000 genomes]
rs4806271	0.89[ASN][1000 genomes]
rs4806273	0.84[ASN][1000 genomes]
rs4806276	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55849299	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250364	0.94[ASN][1000 genomes]
rs7251912	0.92[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs7257026	0.80[ASN][1000 genomes]
rs7258807	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73036134	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112640	0.94[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
rs11669890	ZNF527	cis	cerebellum	SCAN
rs11669890	LOC390940	cis	parietal	SCAN
rs11669890	PHLDB3	cis	parietal	SCAN
rs11669890	CYP2A7	cis	cerebellum	SCAN
rs11669890	ZNF420	cis	cerebellum	SCAN
rs11669890	PHLDB3	cis	cerebellum	SCAN
rs11669890	CYP2A7	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr19:36546600-36572400	Weak transcription	Lung	lung
4	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
5	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
10	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
14	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:36548400-36571000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:36548800-36567800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:36549600-36566600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:36549600-36567200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:36552000-36572400	Weak transcription	Liver	Liver
20	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
21	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
22	chr19:36558200-36572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:36558800-36574000	Weak transcription	Gastric	stomach
24	chr19:36559000-36572400	Weak transcription	Placenta	Placenta
25	chr19:36559200-36570400	Weak transcription	GM12878-XiMat	blood
26	chr19:36559200-36572600	Weak transcription	Fetal Brain Female	brain
27	chr19:36559200-36572800	Weak transcription	Brain Germinal Matrix	brain
28	chr19:36560400-36565800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:36560400-36580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:36560800-36565600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:36561000-36570600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr19:36561000-36572200	Weak transcription	Fetal Intestine Large	intestine
33	chr19:36561200-36569400	Strong transcription	Fetal Stomach	stomach
34	chr19:36561200-36570800	Strong transcription	Thymus	Thymus
35	chr19:36561200-36571000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:36561200-36597600	Strong transcription	Dnd41	blood
40	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:36561400-36564800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:36561600-36567800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:36561600-36572000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:36561800-36566400	Strong transcription	A549	lung
49	chr19:36561800-36569400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:36561800-36572000	Weak transcription	Muscle Satellite Cultured Cells	--

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