Variant report

Variant	rs6499542
Chromosome Location	chr16:71859830-71859831
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71841128..71843403-chr16:71859611..71861303,3	K562	blood:
2	chr16:71841774..71844695-chr16:71859330..71862021,2	MCF-7	breast:
3	chr16:71843627..71847221-chr16:71857601..71861562,3	K562	blood:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11075908	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11859903	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12102548	0.94[CEU][hapmap];0.82[ASN][1000 genomes]
rs12444829	0.81[EUR][1000 genomes]
rs12447045	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12449139	0.82[EUR][1000 genomes]
rs12921084	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13329779	0.83[EUR][1000 genomes]
rs1834034	0.81[EUR][1000 genomes]
rs1834035	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1981874	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288029	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288031	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335709	0.82[EUR][1000 genomes]
rs2335710	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335711	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335712	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2335713	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335714	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335715	0.85[EUR][1000 genomes]
rs3794692	0.81[EUR][1000 genomes]
rs4788445	0.81[AMR][1000 genomes]
rs4788446	0.97[EUR][1000 genomes]
rs4788447	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788449	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788562	0.82[EUR][1000 genomes]
rs4788564	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4788566	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788570	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788571	0.84[EUR][1000 genomes]
rs4788573	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788576	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[EUR][1000 genomes]
rs4788581	0.80[EUR][1000 genomes]
rs4788585	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs62056490	0.92[ASN][1000 genomes]
rs6499533	1.00[JPT][hapmap]
rs6499545	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6499551	0.82[EUR][1000 genomes]
rs6499552	0.83[EUR][1000 genomes]
rs6558	1.00[JPT][hapmap]
rs7184437	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7184486	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7186890	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7187129	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7193731	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194858	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7204708	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7205154	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8044342	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8046859	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8050488	0.80[AMR][1000 genomes]
rs8050651	0.91[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051038	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8057124	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs8058118	0.81[EUR][1000 genomes]
rs8059053	0.81[EUR][1000 genomes]
rs8062946	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8063324	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8063403	0.83[EUR][1000 genomes]
rs9302631	0.83[EUR][1000 genomes]
rs9302632	0.82[EUR][1000 genomes]
rs9806882	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9921412	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9924339	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9937936	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6499542	ZFHX3	cis	cerebellum	SCAN
rs6499542	NRN1L	cis	parietal	SCAN
rs6499542	CMTM4	cis	parietal	SCAN
rs6499542	SNTB2	cis	cerebellum	SCAN
rs6499542	EXOSC6	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71843800-71861600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:71844200-71862200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr16:71844800-71862000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr16:71851000-71860400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr16:71851200-71862200	Weak transcription	Fetal Stomach	stomach
6	chr16:71851200-71866400	Weak transcription	HSMMtube	muscle
7	chr16:71852200-71861600	Weak transcription	Esophagus	oesophagus
8	chr16:71852200-71861800	Weak transcription	Fetal Muscle Leg	muscle
9	chr16:71852200-71861800	Weak transcription	HSMM	muscle
10	chr16:71852200-71866000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr16:71852400-71863000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr16:71852800-71864000	Weak transcription	Osteobl	bone
13	chr16:71853200-71860200	Weak transcription	GM12878-XiMat	blood
14	chr16:71854800-71861200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr16:71856000-71861400	Weak transcription	Psoas Muscle	Psoas
16	chr16:71858000-71863400	Weak transcription	Primary T cells from cord blood	blood
17	chr16:71859600-71860600	ZNF genes & repeats	K562	blood

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