Variant report

Variant	rs6501291
Chromosome Location	chr17:67220454-67220455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr17:67219686-67220611	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ABCA10	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10491177	0.95[JPT][hapmap]
rs112914	0.93[CHD][hapmap]
rs11655507	0.83[CHD][hapmap]
rs11871771	0.86[JPT][hapmap]
rs12939436	0.94[ASN][1000 genomes]
rs1468513	0.95[JPT][hapmap]
rs1860121	0.96[ASN][1000 genomes]
rs475283	0.82[CHB][hapmap]
rs486840	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs534645	0.93[CHD][hapmap]
rs6501292	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs7222780	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs7223895	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs817126	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs9302893	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv457888	chr17:67149973-67226643	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
4	nsv575931	chr17:67149973-67226643	Enhancers Flanking Active TSS Strong transcription Weak 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
5	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
6	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
7	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
8	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6501291	ABCA6	cis	cerebellum	SCAN
rs6501291	PRKAR1A	cis	cerebellum	SCAN
rs6501291	ABCA9	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
2	chr17:67173400-67230000	Weak transcription	Pancreas	Pancrea
3	chr17:67189800-67221400	Weak transcription	Right Ventricle	heart
4	chr17:67207600-67247800	Weak transcription	Left Ventricle	heart
5	chr17:67209800-67223200	Weak transcription	Fetal Muscle Leg	muscle
6	chr17:67213800-67230400	Weak transcription	Brain Angular Gyrus	brain
7	chr17:67215600-67222400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr17:67215600-67222600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr17:67215600-67222600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr17:67215600-67239200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr17:67215600-67249200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:67216800-67224800	Weak transcription	NHDF-Ad	bronchial
13	chr17:67217000-67222000	Weak transcription	Liver	Liver
14	chr17:67218600-67221800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:67218600-67223800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr17:67218800-67221000	Enhancers	Primary T cells from cord blood	blood
17	chr17:67219000-67220800	Enhancers	HepG2	liver
18	chr17:67219200-67221600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:67219400-67220600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:67219400-67221600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:67219600-67220600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:67219800-67220600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr17:67219800-67220800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:67219800-67221600	Active TSS	Ovary	ovary
25	chr17:67219800-67225600	Active TSS	Right Atrium	heart
26	chr17:67220000-67220600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr17:67220000-67224400	Active TSS	Adipose Nuclei	Adipose
28	chr17:67220200-67220600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:67220400-67221200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:67220400-67222600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr17:67220400-67222600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:67220400-67223400	Weak transcription	GM12878-XiMat	blood
33	chr17:67220400-67223600	Weak transcription	Fetal Lung	lung
34	chr17:67220400-67231200	Weak transcription	Osteobl	bone

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