Variant report

Variant	rs2453583
Chromosome Location	chr17:19442036-19442037
allele	A/T
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	chr17:19432886..19434413-chr17:19439676..19442080,2	MCF-7	breast:
4	chr17:19439739..19442461-chr17:19442717..19444481,2	MCF-7	breast:
5	chr17:19434855..19439000-chr17:19439290..19443367,8	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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871125	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2252281	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440164	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453578	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2453579	0.88[EUR][1000 genomes]
rs2453580	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453581	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453582	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453584	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	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8071709	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs894680	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]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2453583	SLC47A1	cis	Nerve Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19438200-19446800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:19438400-19443200	Weak transcription	Lung	lung
3	chr17:19438400-19445600	Weak transcription	A549	lung
4	chr17:19438400-19454400	Weak transcription	Aorta	Aorta
5	chr17:19438400-19456200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:19438800-19446000	Enhancers	Liver	Liver
7	chr17:19440000-19443400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr17:19440200-19442400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr17:19441000-19442400	Enhancers	Left Ventricle	heart
10	chr17:19441000-19442600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr17:19441000-19442800	Enhancers	Brain Cingulate Gyrus	brain
12	chr17:19441000-19442800	Enhancers	Fetal Brain Male	brain
13	chr17:19441000-19442800	Enhancers	Fetal Intestine Large	intestine
14	chr17:19441200-19442200	Weak transcription	Psoas Muscle	Psoas
15	chr17:19441200-19442600	Enhancers	Fetal Intestine Small	intestine
16	chr17:19441200-19442600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr17:19441200-19443600	Enhancers	Brain Hippocampus Middle	brain
18	chr17:19441200-19444400	Enhancers	Fetal Muscle Leg	muscle
19	chr17:19441400-19442200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr17:19441400-19442200	Enhancers	Pancreas	Pancrea
21	chr17:19441400-19442600	Enhancers	Duodenum Mucosa	Duodenum
22	chr17:19441400-19442600	Flanking Active TSS	HepG2	liver
23	chr17:19441400-19442800	Enhancers	Brain Anterior Caudate	brain
24	chr17:19441600-19442200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr17:19441600-19442200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr17:19441600-19442200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr17:19441600-19442200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr17:19441600-19442200	Enhancers	GM12878-XiMat	blood
29	chr17:19441600-19442400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr17:19441600-19442400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:19441600-19442400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr17:19441600-19442400	Enhancers	Right Ventricle	heart
33	chr17:19441600-19442400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr17:19441600-19442600	Weak transcription	Brain Germinal Matrix	brain
35	chr17:19441600-19442600	Enhancers	Fetal Heart	heart
36	chr17:19441600-19443400	Weak transcription	Fetal Brain Female	brain
37	chr17:19441800-19442200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr17:19441800-19442200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr17:19441800-19442400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr17:19441800-19442400	Enhancers	Gastric	stomach
41	chr17:19441800-19442600	Enhancers	Brain Angular Gyrus	brain
42	chr17:19441800-19442800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:19442000-19442200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr17:19442000-19442400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:19442000-19442400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr17:19442000-19442400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr17:19442000-19442400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr17:19442000-19442400	Bivalent Enhancer	HSMMtube	muscle
49	chr17:19442000-19442600	Enhancers	Brain Substantia Nigra	brain
50	chr17:19442000-19442800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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