Variant report

Variant	rs11083566
Chromosome Location	chr19:41245022-41245023
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41243408..41245844-chr19:41255511..41257938,3	MCF-7	breast:
2	chr19:41237958..41241632-chr19:41242031..41245847,4	MCF-7	breast:
3	chr19:41222847..41224765-chr19:41244850..41247375,2	MCF-7	breast:
4	chr19:41237106..41239514-chr19:41244593..41247355,2	K562	blood:
5	chr19:41243259..41245558-chr19:41249121..41252109,2	MCF-7	breast:
6	chr19:41222621..41224327-chr19:41244939..41247313,2	K562	blood:
7	chr19:41231550..41234206-chr19:41242847..41245259,2	MCF-7	breast:
8	chr19:41167265..41169750-chr19:41244881..41246475,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10407351	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425765	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11548478	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976551	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1469427	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1870086	0.82[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1870087	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2115239	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2246095	0.91[JPT][hapmap]
rs2288451	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2290692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2369302	0.82[JPT][hapmap]
rs2604885	0.91[JPT][hapmap]
rs3745210	0.90[ASN][1000 genomes]
rs3745211	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745216	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3865452	0.91[JPT][hapmap]
rs4802085	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4802086	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802087	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803360	0.85[EUR][1000 genomes]
rs7248468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251246	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257602	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7260405	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111960	1.00[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs890934	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11083566	KCNN4	cis	cerebellum	SCAN
rs11083566	LIN7B	cis	parietal	SCAN
rs11083566	C19orf54	cis	Nerve Tibial	GTEx
rs11083566	FOXA3	cis	parietal	SCAN
rs11083566	ZNF574	cis	parietal	SCAN
rs11083566	ADCK4	cis	Nerve Tibial	GTEx
rs11083566	SYMPK	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
6	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
8	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:41228600-41245400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:41228600-41245600	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
15	chr19:41229200-41246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:41229400-41246800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:41229400-41246800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:41229600-41245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:41229600-41246800	Strong transcription	Fetal Lung	lung
22	chr19:41229800-41245600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:41229800-41246400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:41229800-41246800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr19:41229800-41247000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:41229800-41247000	Strong transcription	Liver	Liver
27	chr19:41229800-41247200	Strong transcription	Primary T cells from cord blood	blood
28	chr19:41229800-41248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:41229800-41248600	Strong transcription	Dnd41	blood
30	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
31	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:41230200-41247000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:41230400-41245400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:41230400-41246600	Strong transcription	Left Ventricle	heart
35	chr19:41230400-41247200	Strong transcription	Lung	lung
36	chr19:41230600-41245200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:41230600-41245400	Strong transcription	Stomach Smooth Muscle	stomach
38	chr19:41230800-41245200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:41231000-41245400	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:41231000-41245800	Strong transcription	Brain Hippocampus Middle	brain
41	chr19:41231000-41246200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:41231200-41245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:41231200-41245400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr19:41231600-41245400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:41231600-41245400	Strong transcription	Right Ventricle	heart
46	chr19:41231600-41245800	Strong transcription	Adipose Nuclei	Adipose
47	chr19:41231600-41247000	Strong transcription	Pancreas	Pancrea
48	chr19:41231600-41247400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:41232000-41245800	Strong transcription	Brain Angular Gyrus	brain
50	chr19:41232200-41245800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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