Variant report

Variant	rs11666449
Chromosome Location	chr19:38853659-38853660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:38850909-38853674	A549	lung:	n/a	chr19:38852144-38852154
2	SIX5	chr19:38852638-38853677	A549	lung:	n/a	n/a
3	MAX	chr19:38852161-38853675	H1-hESC	embryonic stem cell:	n/a	chr19:38852622-38852632
4	MAX	chr19:38851469-38853707	A549	lung:	n/a	chr19:38851906-38851913 chr19:38852622-38852632

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38794216..38796351-chr19:38852337..38854290,3	MCF-7	breast:
2	chr19:38851531..38855576-chr19:38863499..38866575,5	MCF-7	breast:
3	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
4	chr19:38851827..38854715-chr19:38877414..38880419,4	K562	blood:
5	chr19:38851103..38853998-chr19:38877778..38880419,3	K562	blood:
6	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
7	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
8	chr19:38826766..38829028-chr19:38851929..38854753,2	K562	blood:
9	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
10	chr19:38851829..38853788-chr19:38876902..38878905,2	MCF-7	breast:
11	chr19:38846299..38848988-chr19:38850348..38854198,4	MCF-7	breast:

No data

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000266963	TF binding region
ENSG00000188766	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000167644	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11668651	0.95[EUR][1000 genomes]
rs11669131	0.91[EUR][1000 genomes]
rs11669230	0.87[EUR][1000 genomes]
rs11672219	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs11673203	0.85[EUR][1000 genomes]
rs12459746	0.94[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs2270093	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2270094	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2270095	0.86[YRI][hapmap]
rs2286473	0.89[EUR][1000 genomes]
rs2302182	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2302183	0.95[EUR][1000 genomes]
rs2304177	0.93[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2368484	0.91[EUR][1000 genomes]
rs2887262	0.92[EUR][1000 genomes]
rs34989303	0.88[EUR][1000 genomes]
rs35308902	0.87[EUR][1000 genomes]
rs3816044	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs3843754	0.86[YRI][hapmap]
rs3900981	0.89[TSI][hapmap]
rs4801723	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802326	0.87[EUR][1000 genomes]
rs4802327	0.93[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs4804016	0.89[EUR][1000 genomes]
rs57681346	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60082376	0.94[EUR][1000 genomes]
rs60487067	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61091932	0.93[EUR][1000 genomes]
rs7256575	0.88[EUR][1000 genomes]
rs8104823	0.89[TSI][hapmap]
rs870218	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11666449	SYCN	cis	parietal	SCAN
rs11666449	APOC4	cis	cerebellum	SCAN
rs11666449	LOC390940	cis	parietal	SCAN
rs11666449	CYP2S1	cis	cerebellum	SCAN
rs11666449	YIF1B	cis	Whole Blood	GTEx
rs11666449	ATP1A3	cis	cerebellum	SCAN
rs11666449	NPAS1	cis	parietal	SCAN
rs11666449	C19orf33	cis	Heart Left Ventricle	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38852200-38853800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr19:38852200-38853800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38852200-38853800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38852200-38853800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
5	chr19:38852200-38853800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:38852400-38853800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:38852400-38853800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:38852400-38853800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr19:38852400-38853800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:38852400-38853800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:38852400-38853800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr19:38852600-38853800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:38852600-38853800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:38852600-38853800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:38852800-38853800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:38852800-38853800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:38852800-38853800	Flanking Active TSS	Colonic Mucosa	Colon
18	chr19:38852800-38853800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr19:38852800-38854000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:38853000-38853800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr19:38853000-38853800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr19:38853000-38853800	Bivalent Enhancer	Fetal Brain Male	brain
23	chr19:38853200-38853800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr19:38853200-38853800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr19:38853200-38853800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:38853200-38853800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr19:38853200-38853800	Enhancers	Lung	lung
28	chr19:38853200-38853800	Enhancers	Spleen	Spleen
29	chr19:38853200-38853800	Flanking Active TSS	K562	blood
30	chr19:38853400-38853800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:38853400-38853800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:38853400-38853800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr19:38853400-38853800	Enhancers	Left Ventricle	heart
34	chr19:38853400-38853800	Enhancers	Pancreas	Pancrea
35	chr19:38853400-38853800	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr19:38853400-38853800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr19:38853400-38853800	Enhancers	Small Intestine	intestine
38	chr19:38853400-38853800	Flanking Active TSS	A549	lung
39	chr19:38853400-38854200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:38853600-38853800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:38853600-38853800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:38853600-38853800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38853600-38853800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:38853600-38853800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:38853600-38853800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr19:38853600-38853800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
47	chr19:38853600-38853800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
48	chr19:38853600-38853800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:38853600-38853800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr19:38853600-38853800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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