Variant report

Variant	rs171994
Chromosome Location	chr1:112637931-112637932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:112636195..112637993-chr1:112640626..112643042,2	MCF-7	breast:
2	chr1:112637048..112640565-chr1:112640927..112645213,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCND3-1	chr1:112635477-112638181	XLOC_000964

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12751286	1.00[ASN][1000 genomes]
rs1372861	1.00[ASN][1000 genomes]
rs1443925	1.00[ASN][1000 genomes]
rs17739527	1.00[ASN][1000 genomes]
rs2819209	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008534	1.00[ASN][1000 genomes]
rs3017628	1.00[ASN][1000 genomes]
rs34751177	1.00[ASN][1000 genomes]
rs367572	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373157	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374902	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374958	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400151	1.00[ASN][1000 genomes]
rs4088223	1.00[ASN][1000 genomes]
rs430680	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432663	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434800	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436173	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436818	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441740	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443625	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs450822	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455228	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457342	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs460443	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461311	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461553	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462936	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463983	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464357	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464819	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466206	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838935	1.00[ASN][1000 genomes]
rs609882	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413702	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831048	chr1:112459697-112680279	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv831059	chr1:112569062-112724725	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831070	chr1:112594658-112792539	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs171994	RSBN1	cis	parietal	SCAN
rs171994	LOC642864	cis	cerebellum	SCAN
rs171994	NHLH2	cis	parietal	SCAN
rs171994	DRAM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112635800-112638000	Enhancers	HUES64 Cell Line	embryonic stem cell

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