Variant report

Variant	rs17863784
Chromosome Location	chr2:234607005-234607006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234394239..234398905-chr2:234606921..234610330,8	MCF-7	breast:
2	chr2:234467119..234468871-chr2:234606248..234608879,2	MCF-7	breast:
3	chr2:234606620..234610585-chr2:234612683..234620351,17	MCF-7	breast:
4	chr2:234382718..234385306-chr2:234606454..234608053,2	MCF-7	breast:
5	chr2:234606390..234610516-chr2:234613313..234618925,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction
ENSG00000224814	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11568318	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1551286	0.84[EUR][1000 genomes]
rs17862835	0.84[EUR][1000 genomes]
rs17862844	0.84[EUR][1000 genomes]
rs17862846	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17862848	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17862851	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862854	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17862859	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17862874	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863786	0.80[YRI][hapmap]
rs17863795	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17863800	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17864666	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17864670	0.84[EUR][1000 genomes]
rs17864671	0.84[EUR][1000 genomes]
rs17864675	0.88[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs17864689	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17864692	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868298	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17868299	0.84[EUR][1000 genomes]
rs17868301	0.84[EUR][1000 genomes]
rs17868318	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17868320	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17868338	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17868341	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17874945	0.81[EUR][1000 genomes]
rs28898581	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28898590	0.87[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34916116	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45507691	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56125405	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56143032	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714486	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6755571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563478	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7585521	0.88[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17863784	ARL4C	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234597800-234608600	Weak transcription	Gastric	stomach
2	chr2:234599400-234608000	Weak transcription	HUVEC	blood vessel
3	chr2:234600400-234608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:234602200-234607600	Weak transcription	Pancreas	Pancrea
5	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:234603400-234608000	Weak transcription	Stomach Mucosa	stomach
7	chr2:234603800-234607600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:234604200-234608600	Weak transcription	HepG2	liver
9	chr2:234605400-234607400	Enhancers	NHEK	skin
10	chr2:234605600-234609000	Enhancers	Liver	Liver
11	chr2:234606600-234608000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:234607000-234607200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:234607000-234607800	Genic enhancers	A549	lung
14	chr2:234607000-234609200	Enhancers	Hela-S3	cervix

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