Variant report

Variant	rs11759658
Chromosome Location	chr6:25359545-25359546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17317669	1.00[ASW][hapmap];0.86[LWK][hapmap];0.82[YRI][hapmap]
rs17678852	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72830715	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366619	0.82[YRI][hapmap]
rs9379757	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379759	0.96[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467471	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11759658	PRSS16	cis	cerebellum	SCAN
rs11759658	PRL	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25335200-25359800	Weak transcription	Thymus	Thymus
2	chr6:25351000-25359600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:25352200-25363000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:25353200-25359600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:25353200-25359600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:25355600-25359600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:25358200-25361000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:25358800-25359600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr6:25358800-25361400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:25358800-25362600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:25359000-25359600	Enhancers	Fetal Heart	heart
12	chr6:25359000-25359600	Enhancers	NHEK	skin
13	chr6:25359000-25360000	Enhancers	Fetal Kidney	kidney
14	chr6:25359000-25360400	Enhancers	Brain Germinal Matrix	brain
15	chr6:25359000-25360800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:25359200-25359600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:25359200-25359600	Enhancers	Adipose Nuclei	Adipose
18	chr6:25359200-25359800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:25359200-25359800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:25359200-25360000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:25359200-25360000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr6:25359200-25360000	Enhancers	Lung	lung
23	chr6:25359200-25360400	Enhancers	Stomach Mucosa	stomach
24	chr6:25359200-25360600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:25359200-25360600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr6:25359200-25360800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:25359200-25361000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:25359200-25361000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:25359200-25361000	Enhancers	Ovary	ovary
30	chr6:25359200-25361000	Enhancers	Small Intestine	intestine
31	chr6:25359200-25361000	Enhancers	A549	lung
32	chr6:25359200-25361200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:25359200-25361200	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:25359200-25361200	Enhancers	HSMM	muscle
35	chr6:25359200-25361400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:25359200-25362800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:25359200-25363600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:25359400-25359600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:25359400-25359600	Flanking Active TSS	Aorta	Aorta
40	chr6:25359400-25359600	Enhancers	Left Ventricle	heart
41	chr6:25359400-25359600	Enhancers	Stomach Smooth Muscle	stomach
42	chr6:25359400-25359800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr6:25359400-25359800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:25359400-25359800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:25359400-25359800	Enhancers	Brain Angular Gyrus	brain
46	chr6:25359400-25359800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:25359400-25359800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
48	chr6:25359400-25359800	Enhancers	Fetal Muscle Trunk	muscle
49	chr6:25359400-25359800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr6:25359400-25359800	Enhancers	Skeletal Muscle Female	skeletal muscle

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