Variant report

Variant	rs1838101
Chromosome Location	chr17:66858055-66858056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1373066	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1443259	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1443261	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1443262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1470292	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1470293	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1470294	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1481	0.92[CEU][hapmap];0.80[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs1550646	0.82[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1808919	0.92[AMR][1000 genomes]
rs1838100	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1867235	0.94[AMR][1000 genomes]
rs1978962	0.84[EUR][1000 genomes]
rs2083790	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2218350	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2363753	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4246431	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4968826	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4968962	0.94[AMR][1000 genomes]
rs4968967	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6501766	0.94[AMR][1000 genomes]
rs6501767	0.94[AMR][1000 genomes]
rs6501768	0.94[AMR][1000 genomes]
rs6501799	0.81[AMR][1000 genomes]
rs6501813	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6501814	0.80[EUR][1000 genomes]
rs6501835	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6501839	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7209220	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7210022	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7211979	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7216817	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8068204	0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8074944	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8078168	0.84[EUR][1000 genomes]
rs8080098	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8082619	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs894593	0.94[AMR][1000 genomes]
rs894594	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs980423	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9895868	0.94[AMR][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1838101	ABCA9	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66850400-66864000	Weak transcription	Ovary	ovary
2	chr17:66856600-66858200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:66857000-66858200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:66857200-66858200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr17:66857200-66858600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr17:66857200-66858600	Enhancers	HUVEC	blood vessel
7	chr17:66857400-66858200	Enhancers	Brain Cingulate Gyrus	brain
8	chr17:66857600-66858200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:66857600-66858200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr17:66857600-66858200	Enhancers	Brain Substantia Nigra	brain
11	chr17:66857600-66858200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr17:66857600-66858200	Enhancers	Small Intestine	intestine
13	chr17:66857800-66858200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:66857800-66858200	Enhancers	Brain Angular Gyrus	brain
15	chr17:66857800-66858800	Enhancers	Fetal Lung	lung
16	chr17:66858000-66858200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr17:66858000-66858200	Enhancers	Adipose Nuclei	Adipose
18	chr17:66858000-66858200	Enhancers	Duodenum Mucosa	Duodenum
19	chr17:66858000-66858200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr17:66858000-66858400	Enhancers	Liver	Liver
21	chr17:66858000-66869800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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