Variant report

Variant	rs1210977
Chromosome Location	chr6:70932535-70932536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70931634..70934194-chr6:71104182..71105989,2	K562	blood:
2	chr6:70930597..70933117-chr6:70988758..70990429,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL19A1-1	chr6:70932461-70932541	ENSG00000253809.1

Variant related genes	Relation type
ENSG00000112280	Chromatin interaction
ENSG00000237643	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10498871	0.84[CEU][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1200569	0.84[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1200576	0.84[CEU][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1200577	0.84[EUR][1000 genomes]
rs12663063	0.84[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16868632	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296006	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2296007	0.82[EUR][1000 genomes]
rs2346212	0.81[EUR][1000 genomes]
rs3806058	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3828775	0.84[MEX][hapmap]
rs4707687	0.81[EUR][1000 genomes]
rs550152	0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs555313	0.84[CEU][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs572716	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58042167	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs583619	0.83[EUR][1000 genomes]
rs58673424	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs622918	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62421668	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62421670	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs624243	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs633762	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs658805	0.84[MEX][hapmap]
rs7756657	0.84[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7765390	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs809074	0.82[EUR][1000 genomes]
rs9454995	0.84[CEU][hapmap];0.82[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
rs1210977	C6orf57	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70931400-70934800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:70931400-70961400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:70932400-70932600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:70932400-70938000	Weak transcription	Fetal Brain Female	brain

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