Variant report

Variant	rs17267523
Chromosome Location	chr13:93900848-93900849
allele	A/G
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	chr13:93899798..93901892-chr9:134131484..134133975,2	K562	blood:
2	chr13:93900783..93902371-chr13:108518560..108520296,2	K562	blood:
3	chr13:93896826..93900351-chr13:93900549..93903054,4	K562	blood:
4	chr13:93899582..93901568-chr13:108550568..108552449,2	K562	blood:
5	chr13:93877323..93880344-chr13:93900114..93902371,3	MCF-7	breast:
6	chr13:93894789..93899611-chr13:93899761..93903867,5	K562	blood:
7	chr13:93900253..93901770-chr13:93904316..93907177,2	K562	blood:
8	chr13:93899962..93902083-chr13:108641328..108643752,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204442	Chromatin interaction
ENSG00000183098	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1008993	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1328366	0.88[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1328370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16948547	0.95[CEU][hapmap];0.96[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs17188802	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17645969	0.83[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs17645998	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17702471	1.00[LWK][hapmap];0.83[TSI][hapmap]
rs2209880	0.82[GIH][hapmap];1.00[LWK][hapmap];0.80[TSI][hapmap]
rs59772512	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61963718	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61963740	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61963741	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61963744	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61963746	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61963747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61963748	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61965664	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61965665	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72633947	0.82[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
rs17267523	GPC6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93891600-93901200	Weak transcription	Fetal Intestine Small	intestine
2	chr13:93897000-93901000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:93897000-93904200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:93897000-93910400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:93897200-93901000	Weak transcription	Fetal Kidney	kidney
6	chr13:93897200-93901000	Weak transcription	Right Atrium	heart
7	chr13:93897200-93902800	Weak transcription	Fetal Stomach	stomach
8	chr13:93897200-93923000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:93897400-93901000	Weak transcription	NHLF	lung
10	chr13:93897400-93907000	Weak transcription	Aorta	Aorta
11	chr13:93897600-93901400	Weak transcription	NHEK	skin
12	chr13:93897800-93901000	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:93898000-93901000	Weak transcription	HSMMtube	muscle
14	chr13:93898000-93901200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:93898200-93901200	Weak transcription	HMEC	breast
16	chr13:93898200-93901600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:93898400-93901400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:93898400-93901400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:93898400-93902200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:93898600-93901000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr13:93898600-93901000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:93898600-93901000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:93898600-93901000	Weak transcription	HSMM	muscle
24	chr13:93898600-93901200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr13:93899800-93901000	Weak transcription	Liver	Liver
26	chr13:93899800-93903200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:93900400-93901000	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr13:93900400-93902200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr13:93900600-93901000	Weak transcription	Brain Germinal Matrix	brain
30	chr13:93900600-93902000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr13:93900600-93902400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr13:93900800-93901000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr13:93900800-93901200	Enhancers	Psoas Muscle	Psoas
34	chr13:93900800-93901200	Active TSS	A549	lung
35	chr13:93900800-93901200	Active TSS	HepG2	liver
36	chr13:93900800-93901200	Enhancers	NH-A	brain
37	chr13:93900800-93901400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr13:93900800-93901400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:93900800-93901400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:93900800-93901600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:93900800-93901600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr13:93900800-93901800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:93900800-93901800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr13:93900800-93902000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:93900800-93902200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr13:93900800-93902200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr13:93900800-93902200	Enhancers	K562	blood
48	chr13:93900800-93902600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:93900800-93903200	Enhancers	Osteobl	bone
50	chr13:93900800-93903600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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