Variant report

Variant	rs814875
Chromosome Location	chr1:76109573-76109574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:76109231-76109653	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76103722..76106233-chr1:76108885..76111145,2	K562	blood:
2	chr1:76102793..76106233-chr1:76108594..76111145,3	K562	blood:

Variant related genes	Relation type
ENSG00000230863	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11161465	0.95[CEU][hapmap]
rs11163917	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11163928	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11164035	0.88[CEU][hapmap]
rs1146634	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs1146635	0.84[GIH][hapmap]
rs1146636	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs1146644	0.91[GIH][hapmap];0.86[TSI][hapmap]
rs12022011	1.00[CEU][hapmap]
rs12044025	0.90[CEU][hapmap]
rs12045299	0.95[CEU][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap]
rs12732722	0.95[CEU][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap]
rs12744608	0.95[CEU][hapmap]
rs1323735	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1332786	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1463812	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs211709	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211712	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211715	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211716	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211719	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211721	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211722	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211736	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6695055	0.95[CEU][hapmap]
rs7533542	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7548991	0.95[CEU][hapmap]
rs7552289	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs814853	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs814857	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs814860	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs814861	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs814871	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs814872	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs814876	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs9660848	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv2756846	chr1:76083408-76156986	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv10295	chr1:76085406-76119292	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv997990	chr1:76086763-76121738	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1003742	chr1:76086763-76124052	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv998205	chr1:76086763-76125366	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv3692758	chr1:76088392-76126205	Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv546582	chr1:76088392-76126205	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv546583	chr1:76088392-76134765	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	esv34738	chr1:76094234-76121479	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv34562	chr1:76094234-76121738	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs814875	MSH4	cis	cerebellum	SCAN
rs814875	RABGGTB	cis	lymphoblastoid	seeQTL
rs814875	MSH4	cis	parietal	SCAN
rs814875	RABGGTB	cis	multi-tissue	Pritchard
rs814875	MSH4	cis	Muscle Skeletal	GTEx
rs814875	AK5	cis	parietal	SCAN
rs814875	ACADM	cis	cerebellum	SCAN
rs814875	RABGGTB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76109200-76109800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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