Variant report

Variant	rs12451886
Chromosome Location	chr17:17200241-17200242
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	chr17:17184001..17186220-chr17:17199204..17203201,3	K562	blood:
2	chr17:17198944..17201755-chr17:17206593..17208190,2	K562	blood:

Variant related genes	Relation type
ENSG00000141030	Chromatin interaction
ENSG00000205309	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2041393	0.98[ASN][1000 genomes]
rs62066114	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62066115	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502577	0.80[ASN][1000 genomes]
rs6502578	0.80[ASN][1000 genomes]
rs7207856	0.98[ASN][1000 genomes]
rs7217114	0.84[ASN][1000 genomes]
rs7217162	0.84[ASN][1000 genomes]
rs9889367	0.82[ASN][1000 genomes]
rs9889738	0.82[ASN][1000 genomes]
rs9895057	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9896977	0.80[ASN][1000 genomes]
rs9899615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907528	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9907711	0.83[ASN][1000 genomes]
rs9907857	0.83[ASN][1000 genomes]
rs9908360	0.80[ASN][1000 genomes]
rs9908807	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9909032	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9909111	0.83[ASN][1000 genomes]
rs9912109	0.89[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv33859	chr17:17189904-17208157	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12451886	SNORD49A	cis	cerebellum	SCAN
rs12451886	PRPSAP2	cis	cerebellum	SCAN
rs12451886	SMCR7	cis	parietal	SCAN
rs12451886	MAPK7	cis	parietal	SCAN
rs12451886	FLII	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17199600-17200400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr17:17199600-17200400	Enhancers	HMEC	breast
3	chr17:17199600-17201000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr17:17199600-17201000	Enhancers	NHLF	lung
5	chr17:17199600-17201200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:17199600-17202200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:17199600-17202200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:17199600-17202200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr17:17199600-17202200	Enhancers	Osteobl	bone
10	chr17:17199600-17202400	Enhancers	GM12878-XiMat	blood
11	chr17:17199800-17200400	Enhancers	A549	lung
12	chr17:17199800-17200800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:17199800-17201000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr17:17199800-17201200	Enhancers	NHDF-Ad	bronchial
15	chr17:17199800-17203800	Weak transcription	Fetal Muscle Leg	muscle
16	chr17:17200000-17200400	Enhancers	NHEK	skin
17	chr17:17200000-17200600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:17200000-17200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:17200000-17203400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:17200000-17203600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr17:17200000-17203600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:17200200-17201600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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