Variant report

Variant	rs894680
Chromosome Location	chr17:19440538-19440539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19440168..19441762-chr17:19550485..19553187,2	MCF-7	breast:
2	chr17:19432886..19434413-chr17:19439676..19442080,2	MCF-7	breast:
3	chr17:19439739..19442461-chr17:19442717..19444481,2	MCF-7	breast:
4	chr17:19434855..19439000-chr17:19439290..19443367,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142494	Chromatin interaction
ENSG00000264932	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11870808	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871125	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252281	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440164	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440165	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453578	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2453579	0.87[EUR][1000 genomes]
rs2453580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453584	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55661368	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8071709	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs894682	0.97[ASN][1000 genomes]

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	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs894680	C17orf76	cis	cerebellum	SCAN
rs894680	NCOR1	cis	cerebellum	SCAN
rs894680	NT5M	cis	cerebellum	SCAN
rs894680	SLC47A1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19437800-19441400	Weak transcription	Pancreas	Pancrea
2	chr17:19437800-19441800	Weak transcription	Gastric	stomach
3	chr17:19438000-19442000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:19438200-19441600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr17:19438200-19446800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:19438400-19441000	Weak transcription	Left Ventricle	heart
7	chr17:19438400-19441600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr17:19438400-19441600	Weak transcription	GM12878-XiMat	blood
9	chr17:19438400-19442000	Weak transcription	Brain Substantia Nigra	brain
10	chr17:19438400-19443200	Weak transcription	Lung	lung
11	chr17:19438400-19445600	Weak transcription	A549	lung
12	chr17:19438400-19454400	Weak transcription	Aorta	Aorta
13	chr17:19438400-19456200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:19438800-19441200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr17:19438800-19446000	Enhancers	Liver	Liver
16	chr17:19439800-19441000	Flanking Active TSS	HepG2	liver
17	chr17:19440000-19443400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr17:19440200-19441200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:19440200-19442000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr17:19440200-19442400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr17:19440400-19440600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr17:19440400-19440600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:19440400-19440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr17:19440400-19441200	Enhancers	Psoas Muscle	Psoas
25	chr17:19440400-19441800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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