Variant report

Variant	rs1443261
Chromosome Location	chr17:66878378-66878379
allele	A/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	CTCF	chr17:66878340-66878490	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:66873136..66876318-chr17:66877176..66880120,3	MCF-7	breast:

Variant related genes	Relation type
ABCA8	TF binding region
ENSG00000141338	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1373066	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1443259	0.94[AMR][1000 genomes]
rs1443262	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1470292	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470293	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1470294	0.94[AMR][1000 genomes]
rs1481	0.96[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1808919	0.86[AMR][1000 genomes]
rs1838100	0.94[AMR][1000 genomes]
rs1838101	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1867235	0.89[AMR][1000 genomes]
rs2083790	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2218350	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2363753	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4246431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4968826	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4968962	0.89[AMR][1000 genomes]
rs4968967	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6501766	0.89[AMR][1000 genomes]
rs6501767	0.89[AMR][1000 genomes]
rs6501768	0.89[AMR][1000 genomes]
rs6501813	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6501835	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6501839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7209220	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7210022	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7211979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7216817	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8068204	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8074944	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8080098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8082619	0.94[AMR][1000 genomes]
rs894593	0.89[AMR][1000 genomes]
rs894594	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980423	0.94[AMR][1000 genomes]
rs9895868	0.89[AMR][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	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	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv908695	chr17:66865583-66904001	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1443261	ABCA9	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66866800-66883600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:66869200-66903400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr17:66869800-66883400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:66873400-66880800	Strong transcription	Fetal Lung	lung
5	chr17:66875400-66881200	Strong transcription	Psoas Muscle	Psoas
6	chr17:66875600-66881400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:66876000-66878400	ZNF genes & repeats	Brain Angular Gyrus	brain
8	chr17:66876200-66882600	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:66876400-66878600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:66877000-66878400	Strong transcription	Fetal Heart	heart
11	chr17:66877000-66879800	Strong transcription	Brain Cingulate Gyrus	brain
12	chr17:66877000-66880600	Weak transcription	Right Ventricle	heart
13	chr17:66877000-66881200	Strong transcription	Brain Substantia Nigra	brain
14	chr17:66877000-66881400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr17:66877000-66882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:66877000-66883800	Strong transcription	Adipose Nuclei	Adipose
17	chr17:66877000-66884000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr17:66877000-66886200	Weak transcription	Colonic Mucosa	Colon
19	chr17:66877000-66886600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:66877000-66889000	Weak transcription	Spleen	Spleen
21	chr17:66877000-66906200	Weak transcription	Fetal Stomach	stomach
22	chr17:66877200-66882000	Strong transcription	Left Ventricle	heart
23	chr17:66877200-66882400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr17:66877200-66882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:66877200-66887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:66877400-66882600	Weak transcription	Placenta	Placenta
27	chr17:66877600-66881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:66877600-66888400	Strong transcription	Liver	Liver
29	chr17:66877600-66893400	Weak transcription	Brain Anterior Caudate	brain
30	chr17:66877800-66879400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr17:66877800-66880000	Strong transcription	Brain Hippocampus Middle	brain
32	chr17:66877800-66880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:66877800-66918200	Weak transcription	Fetal Brain Male	brain
34	chr17:66878000-66880000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:66878200-66878400	Enhancers	Esophagus	oesophagus
36	chr17:66878200-66879000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr17:66878200-66879400	Weak transcription	Fetal Muscle Leg	muscle
38	chr17:66878200-66880800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:66878200-66881800	Strong transcription	Ovary	ovary
40	chr17:66878200-66889400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr17:66878200-66899200	Weak transcription	Osteobl	bone

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