Variant report

Variant	rs7222780
Chromosome Location	chr17:67230586-67230587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66759937..66761790-chr17:67229157..67232001,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10491177	0.86[JPT][hapmap]
rs112914	0.82[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs11655507	0.81[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.80[ASN][1000 genomes]
rs11871771	0.95[JPT][hapmap]
rs12938039	0.83[JPT][hapmap]
rs12939436	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1468513	0.86[JPT][hapmap]
rs1860121	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471193	0.87[AMR][1000 genomes]
rs475283	0.82[CHB][hapmap]
rs486840	0.83[MEX][hapmap]
rs531586	0.86[AMR][1000 genomes]
rs534645	0.95[CHD][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs6501291	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs6501292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6501313	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7223895	0.83[MEX][hapmap]
rs817121	0.87[AMR][1000 genomes]
rs817126	0.83[MEX][hapmap]
rs817128	0.87[AMR][1000 genomes]
rs9302893	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv516799	chr17:67210267-67231581	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7222780	ABCA8	cis	parietal	SCAN
rs7222780	ABCA6	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
2	chr17:67207600-67247800	Weak transcription	Left Ventricle	heart
3	chr17:67215600-67239200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr17:67215600-67249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:67220400-67231200	Weak transcription	Osteobl	bone
6	chr17:67223000-67235600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:67224600-67248600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr17:67225200-67231600	Weak transcription	Ovary	ovary
9	chr17:67226800-67236400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:67229400-67233200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:67229600-67231200	Weak transcription	Brain Anterior Caudate	brain
12	chr17:67230000-67230600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:67230000-67230600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
14	chr17:67230000-67230800	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr17:67230000-67230800	ZNF genes & repeats	Pancreas	Pancrea
16	chr17:67230200-67230600	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr17:67230200-67230800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:67230200-67230800	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr17:67230200-67235800	Weak transcription	Fetal Lung	lung
20	chr17:67230400-67230600	ZNF genes & repeats	Fetal Intestine Large	intestine
21	chr17:67230400-67230800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr17:67230400-67231000	Enhancers	Brain Angular Gyrus	brain
23	chr17:67230400-67231200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr17:67230400-67231400	Weak transcription	NHDF-Ad	bronchial
25	chr17:67230400-67231800	Enhancers	Brain Hippocampus Middle	brain

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