Variant report

Variant	rs17071545
Chromosome Location	chr13:80090114-80090115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80088753..80091957-chr13:80093652..80097974,3	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1475797	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs1577416	1.00[YRI][hapmap]
rs17071512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2760105	1.00[YRI][hapmap]
rs2783119	1.00[YRI][hapmap]
rs3742119	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3903388	1.00[YRI][hapmap]
rs61342959	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73234699	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7338530	1.00[YRI][hapmap]
rs9318626	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs9318627	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs9545087	1.00[YRI][hapmap]
rs9545097	1.00[YRI][hapmap]
rs9545101	1.00[YRI][hapmap]
rs9574413	1.00[YRI][hapmap]
rs9574422	1.00[YRI][hapmap]

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	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv916983	chr13:80065879-80249702	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17071545	SLAIN1	cis	cerebellum	SCAN
rs17071545	TBC1D4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80066800-80122800	Weak transcription	Esophagus	oesophagus
2	chr13:80067200-80095000	Weak transcription	HSMM	muscle
3	chr13:80070600-80096600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:80076000-80099200	Weak transcription	Hela-S3	cervix
5	chr13:80076200-80093200	Weak transcription	HMEC	breast
6	chr13:80077600-80095600	Weak transcription	Fetal Intestine Large	intestine
7	chr13:80078000-80097200	Weak transcription	Psoas Muscle	Psoas
8	chr13:80078000-80097800	Weak transcription	Ovary	ovary
9	chr13:80078200-80102000	Weak transcription	Right Ventricle	heart
10	chr13:80079600-80098200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:80082800-80092400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:80082800-80096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr13:80082800-80096600	Weak transcription	Lung	lung
14	chr13:80082800-80108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:80083000-80095200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:80083000-80120000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:80083000-80122800	Weak transcription	Stomach Mucosa	stomach
18	chr13:80083200-80095000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:80083200-80095000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:80083400-80092200	Weak transcription	NHEK	skin
21	chr13:80083400-80093000	Weak transcription	Right Atrium	heart
22	chr13:80083400-80096200	Weak transcription	Left Ventricle	heart
23	chr13:80085000-80093000	Weak transcription	Fetal Intestine Small	intestine
24	chr13:80085000-80096800	Weak transcription	Primary T cells from cord blood	blood
25	chr13:80086000-80090800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:80086200-80091000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr13:80086800-80098400	Weak transcription	Brain Substantia Nigra	brain
28	chr13:80087000-80095000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr13:80087400-80090400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:80087400-80092800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:80087400-80093800	Enhancers	Dnd41	blood
32	chr13:80087400-80095200	Weak transcription	Liver	Liver
33	chr13:80087400-80134000	Weak transcription	Aorta	Aorta
34	chr13:80087400-80134600	Weak transcription	Pancreas	Pancrea
35	chr13:80087800-80095000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:80087800-80096600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr13:80088000-80095200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr13:80088600-80091600	Enhancers	Fetal Heart	heart
39	chr13:80089000-80096600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr13:80089200-80098800	Weak transcription	Brain Angular Gyrus	brain
41	chr13:80089400-80091200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:80089400-80097800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:80089400-80098800	Weak transcription	Brain Anterior Caudate	brain
44	chr13:80089400-80098800	Weak transcription	Brain Hippocampus Middle	brain
45	chr13:80089400-80099200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr13:80089400-80118400	Weak transcription	Small Intestine	intestine
47	chr13:80089800-80094800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr13:80090000-80095000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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