Variant report

Variant	rs17645969
Chromosome Location	chr13:93879390-93879391
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:93871860..93874254-chr13:93879384..93881257,3	K562	blood:
2	chr13:93879207..93881575-chr4:6694690..6696202,2	MCF-7	breast:
3	chr13:93879341..93882111-chr13:94847801..94850206,2	MCF-7	breast:
4	chr13:93879154..93880951-chr13:93922724..93924964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163993	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008993	0.81[CEU][hapmap]
rs1328366	0.87[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap]
rs1328370	0.83[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs16948547	0.81[TSI][hapmap]
rs17188802	0.81[EUR][1000 genomes]
rs17267523	0.83[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs17645998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17702471	0.84[CEU][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2004191	0.95[AFR][1000 genomes]
rs2209880	0.84[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4400921	0.81[EUR][1000 genomes]
rs61963718	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61963740	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61963741	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61963744	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61963746	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61963747	0.82[EUR][1000 genomes]
rs61963748	0.81[EUR][1000 genomes]
rs72633947	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181846	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs9561276	0.85[AFR][1000 genomes]
rs9561281	0.84[EUR][1000 genomes]
rs970617	0.84[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17645969	GPC6	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93878000-93881600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr13:93878000-93882800	Active TSS	Aorta	Aorta
3	chr13:93878200-93880600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:93878200-93881000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr13:93878200-93881600	Active TSS	Colon Smooth Muscle	Colon
6	chr13:93878200-93881600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr13:93878200-93882200	Active TSS	Fetal Brain Male	brain
8	chr13:93878200-93882800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr13:93878400-93880200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr13:93878400-93881400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:93878400-93881400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:93878400-93881400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:93878400-93881400	Active TSS	Rectal Smooth Muscle	rectum
14	chr13:93878400-93881600	Active TSS	Brain Anterior Caudate	brain
15	chr13:93878400-93881600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr13:93878400-93882000	Active TSS	Ovary	ovary
17	chr13:93878400-93882400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:93878400-93882600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:93878600-93879400	Active TSS	Fetal Muscle Trunk	muscle
20	chr13:93878600-93879600	Active TSS	Brain Substantia Nigra	brain
21	chr13:93878600-93879800	Active TSS	Adipose Nuclei	Adipose
22	chr13:93878600-93881000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr13:93878600-93881000	Bivalent/Poised TSS	Psoas Muscle	Psoas
24	chr13:93878600-93881200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:93878600-93881200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr13:93878600-93881200	Active TSS	Brain Angular Gyrus	brain
27	chr13:93878600-93881400	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr13:93878600-93881600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:93878600-93881600	Active TSS	Brain Cingulate Gyrus	brain
30	chr13:93878600-93881600	Active TSS	HSMM	muscle
31	chr13:93878600-93881800	Active TSS	NHDF-Ad	bronchial
32	chr13:93878600-93881800	Active TSS	Osteobl	bone
33	chr13:93878600-93882000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:93878600-93882000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:93878600-93882000	Active TSS	Fetal Intestine Large	intestine
36	chr13:93878600-93882200	Active TSS	Brain Germinal Matrix	brain
37	chr13:93878600-93882400	Active TSS	NHLF	lung
38	chr13:93878800-93879400	Active TSS	Right Ventricle	heart
39	chr13:93878800-93879600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
40	chr13:93878800-93879600	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr13:93878800-93880600	Active TSS	Liver	Liver
42	chr13:93878800-93880800	Bivalent/Poised TSS	K562	blood
43	chr13:93878800-93881000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
44	chr13:93878800-93881000	Active TSS	Fetal Heart	heart
45	chr13:93878800-93881200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr13:93878800-93881200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr13:93878800-93881200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:93878800-93881200	Bivalent/Poised TSS	Fetal Thymus	thymus
49	chr13:93878800-93881200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:93878800-93881400	Active TSS	H9 Cell Line	embryonic stem cell

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