Variant report

Variant	rs544179
Chromosome Location	chr6:70940822-70940823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1135056	0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.92[ASN][1000 genomes]
rs113979	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1200579	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200580	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153874	0.85[EUR][1000 genomes]
rs12153902	0.86[EUR][1000 genomes]
rs12191701	0.89[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs12195968	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12209857	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs12213613	0.83[EUR][1000 genomes]
rs1753208	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2024730	0.84[CEU][hapmap]
rs2176356	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2182999	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2274586	0.89[ASN][1000 genomes]
rs500457	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs507676	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs516166	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519068	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs528080	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs535308	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs538588	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs546628	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550675	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap]
rs555663	0.90[MEX][hapmap]
rs590656	0.85[MEX][hapmap]
rs59322080	0.87[EUR][1000 genomes]
rs657572	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919444	0.90[EUR][1000 genomes]
rs6922941	0.86[EUR][1000 genomes]
rs6932776	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs701686	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs701688	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs701689	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs701690	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs701693	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7741471	0.91[EUR][1000 genomes]
rs7759110	0.85[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	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs544179	C6orf57	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70931400-70961400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:70932600-70951800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:70933000-70951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:70933600-70947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:70934400-70951600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:70938400-70941000	Enhancers	Fetal Brain Male	brain
7	chr6:70939000-70951600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:70939600-70942200	Weak transcription	Fetal Brain Female	brain
9	chr6:70939600-70942800	Enhancers	Fetal Stomach	stomach
10	chr6:70940600-70941800	Enhancers	Brain Germinal Matrix	brain

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