Variant report

Variant	rs1519073
Chromosome Location	chr11:107986418-107986419
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107984261..107988024-chr11:107989192..107992073,3	K562	blood:
2	chr11:107878617..107881066-chr11:107984671..107987003,3	K562	blood:

Variant related genes	Relation type
ENSG00000166266	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11212484	0.87[CEU][hapmap]
rs11212524	0.81[YRI][hapmap]
rs11212525	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11212551	0.82[JPT][hapmap]
rs11605442	0.83[JPT][hapmap]
rs12360727	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12786416	0.86[AMR][1000 genomes]
rs12787445	0.84[CHD][hapmap]
rs12794010	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1550609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs183459	0.82[JPT][hapmap]
rs183460	0.82[JPT][hapmap]
rs1850730	0.82[JPT][hapmap]
rs2070661	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2083707	0.82[JPT][hapmap]
rs228589	0.82[JPT][hapmap]
rs34971817	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736509	0.83[CEU][hapmap]
rs3781868	0.85[JPT][hapmap]
rs4028262	0.87[CEU][hapmap]
rs4623864	0.82[JPT][hapmap]
rs4754305	0.82[JPT][hapmap]
rs609557	0.82[JPT][hapmap]
rs6589007	0.82[JPT][hapmap]
rs7118967	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7931681	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1519073	NPAT	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107953200-107991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:107955800-107991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:107966400-107992000	Weak transcription	Fetal Brain Male	brain
4	chr11:107967000-107991400	Weak transcription	A549	lung
5	chr11:107968200-107986800	Weak transcription	Colonic Mucosa	Colon
6	chr11:107968200-107992000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:107969000-107991600	Weak transcription	Hela-S3	cervix
8	chr11:107969200-107991800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:107970600-107991600	Weak transcription	HepG2	liver
10	chr11:107972400-107991400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:107972400-107991600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:107972400-107992000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:107972600-107992200	Weak transcription	Gastric	stomach
14	chr11:107973400-107991800	Weak transcription	Primary T cells from cord blood	blood
15	chr11:107973600-107991600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:107973600-107991800	Weak transcription	Primary B cells from cord blood	blood
17	chr11:107973600-107991800	Weak transcription	Brain Germinal Matrix	brain
18	chr11:107973600-107991800	Weak transcription	Fetal Brain Female	brain
19	chr11:107973800-107986600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:107973800-107991600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:107973800-107991800	Weak transcription	Lung	lung
22	chr11:107973800-107992000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:107974200-107991800	Weak transcription	Thymus	Thymus
24	chr11:107974600-107991800	Weak transcription	HUVEC	blood vessel
25	chr11:107974800-107992000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:107975400-107991600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr11:107975400-107991800	Weak transcription	Fetal Intestine Large	intestine
28	chr11:107975400-107991800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:107975400-107991800	Weak transcription	GM12878-XiMat	blood
30	chr11:107975600-107991400	Weak transcription	Dnd41	blood
31	chr11:107975800-107991600	Weak transcription	Placenta	Placenta
32	chr11:107975800-107991800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:107976600-107991800	Weak transcription	Fetal Thymus	thymus
34	chr11:107977000-107991400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:107977000-107991800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr11:107977200-107991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:107977200-107991600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:107977200-107991800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:107977800-107991800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:107978200-107991800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:107980200-107991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:107981600-107991800	Weak transcription	Fetal Intestine Small	intestine
43	chr11:107982400-107991800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:107982600-107986600	Weak transcription	Fetal Stomach	stomach
45	chr11:107984800-107987400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr11:107985000-107987600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:107985200-107986800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:107985200-107987400	Enhancers	Psoas Muscle	Psoas
49	chr11:107985400-107987000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:107985400-107987000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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