Variant report

Variant	rs2453584
Chromosome Location	chr17:19443445-19443446
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:19440630..19443523-chr17:19445687..19447699,2	MCF-7	breast:
2	chr17:19440634..19444214-chr17:19454168..19459092,4	MCF-7	breast:
3	chr17:19439739..19442461-chr17:19442717..19444481,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142494	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11870808	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11871125	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2440164	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2440165	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453578	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2453579	0.84[EUR][1000 genomes]
rs2453580	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2453581	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2453582	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2453583	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55661368	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8071709	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs894680	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]
rs894682	0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2453584	SLC47A1	cis	Nerve Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19438200-19446800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:19438400-19445600	Weak transcription	A549	lung
3	chr17:19438400-19454400	Weak transcription	Aorta	Aorta
4	chr17:19438400-19456200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:19438800-19446000	Enhancers	Liver	Liver
6	chr17:19441200-19443600	Enhancers	Brain Hippocampus Middle	brain
7	chr17:19441200-19444400	Enhancers	Fetal Muscle Leg	muscle
8	chr17:19442000-19447600	Weak transcription	Spleen	Spleen
9	chr17:19442000-19448000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:19442200-19443600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:19442200-19447400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr17:19442400-19447400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr17:19442400-19451200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:19442400-19451200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:19442400-19451400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:19442600-19443600	Enhancers	Fetal Muscle Trunk	muscle
17	chr17:19442600-19443600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr17:19442600-19443600	Enhancers	HepG2	liver
19	chr17:19442600-19444000	Enhancers	Brain Germinal Matrix	brain
20	chr17:19442600-19444400	Weak transcription	Fetal Heart	heart
21	chr17:19442600-19449000	Weak transcription	Fetal Intestine Small	intestine
22	chr17:19442800-19443600	Enhancers	Psoas Muscle	Psoas
23	chr17:19442800-19446800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:19443000-19443600	Enhancers	Fetal Stomach	stomach
25	chr17:19443200-19443600	Enhancers	Fetal Brain Male	brain
26	chr17:19443400-19443600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
27	chr17:19443400-19443600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr17:19443400-19443600	Bivalent Enhancer	HSMMtube	muscle
29	chr17:19443400-19443800	Enhancers	Fetal Brain Female	brain
30	chr17:19443400-19446600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:19443400-19461200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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