Variant report

Variant	rs740519
Chromosome Location	chr17:67147950-67147951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11657620	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11657804	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12950035	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7504026	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs740519	ABCA6	cis	parietal	SCAN
rs740519	TEX2	cis	parietal	SCAN
rs740519	PSMC5	cis	parietal	SCAN
rs740519	ABCA6	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
2	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:67127000-67150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:67132000-67151600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr17:67138000-67154000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr17:67138200-67150600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:67138200-67151200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr17:67138200-67151600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:67138200-67152200	Weak transcription	Fetal Muscle Leg	muscle
10	chr17:67138600-67155400	Weak transcription	Brain Anterior Caudate	brain
11	chr17:67138800-67152000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:67138800-67162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:67138800-67182000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:67140200-67154000	Weak transcription	Fetal Lung	lung
15	chr17:67141600-67155400	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:67141800-67171800	Weak transcription	GM12878-XiMat	blood
17	chr17:67142000-67148800	Weak transcription	NHDF-Ad	bronchial
18	chr17:67142200-67152400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:67142400-67151000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:67143800-67154200	Weak transcription	Right Ventricle	heart
21	chr17:67144000-67148600	Weak transcription	Spleen	Spleen
22	chr17:67144000-67151600	Weak transcription	Fetal Intestine Large	intestine
23	chr17:67144000-67163200	Weak transcription	Left Ventricle	heart
24	chr17:67144000-67175800	Weak transcription	Gastric	stomach
25	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
26	chr17:67144800-67150400	Strong transcription	Liver	Liver
27	chr17:67145000-67150200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:67146000-67148400	Weak transcription	Pancreas	Pancrea
29	chr17:67146800-67148800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr17:67147400-67148200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:67147400-67148400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:67147400-67150800	Strong transcription	Ovary	ovary
33	chr17:67147600-67150800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr17:67147600-67151400	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:67147800-67148600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:67147800-67150600	Strong transcription	Adipose Nuclei	Adipose

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