Variant report

Variant	rs17690664
Chromosome Location	chr10:18701678-18701679
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18688539..18692004-chr10:18698715..18701729,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165995	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10508561	0.84[GIH][hapmap]
rs11014026	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs11014084	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11014144	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11014156	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11014175	0.87[CEU][hapmap];0.84[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11014188	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11014200	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11014208	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11014209	0.81[JPT][hapmap]
rs11014210	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11014211	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11014299	0.80[CHB][hapmap]
rs12049663	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16917251	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3750592	0.85[JPT][hapmap]
rs3829133	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61839258	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61841960	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61842000	0.83[ASN][1000 genomes]
rs6482438	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs67214975	0.82[ASN][1000 genomes]
rs7096168	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72786093	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7477742	0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17690664	ARHGEF12	trans	cerebellum	SCAN
rs17690664	CACNB2	cis	cerebellum	SCAN
rs17690664	TRDMT1	cis	parietal	SCAN
rs17690664	NSUN6	cis	cerebellum	SCAN
rs17690664	SUV39H2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18690000-18703600	Weak transcription	Fetal Stomach	stomach
2	chr10:18690000-18705600	Weak transcription	Aorta	Aorta
3	chr10:18690200-18713000	Weak transcription	Ovary	ovary
4	chr10:18690600-18702800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:18691000-18702600	Weak transcription	Pancreas	Pancrea
6	chr10:18692000-18702600	Weak transcription	Liver	Liver
7	chr10:18692000-18712600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:18692400-18703000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:18692600-18702800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:18692600-18707600	Weak transcription	Brain Angular Gyrus	brain
11	chr10:18696400-18702800	Weak transcription	Right Ventricle	heart
12	chr10:18699000-18703000	Weak transcription	Fetal Intestine Large	intestine
13	chr10:18700000-18703600	Enhancers	Fetal Heart	heart
14	chr10:18700600-18703000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:18701000-18702800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:18701000-18705800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:18701200-18702800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:18701200-18702800	Weak transcription	Left Ventricle	heart
19	chr10:18701200-18702800	Weak transcription	Lung	lung
20	chr10:18701600-18701800	Enhancers	Colon Smooth Muscle	Colon

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