Variant report

Variant	rs12745456
Chromosome Location	chr1:76108055-76108056
allele	C/T
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	STAT3	chr1:76108001-76108189	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC44A5-4	chr1:76107988-76108177	NONHSAT003985
2	lnc-SLC44A5-4	chr1:76105925-76108177	NONHSAT003984

Variant related genes	Relation type
ENSG00000230863	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10489587	1.00[ASW][hapmap]
rs10782556	0.82[ASN][1000 genomes]
rs10873738	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11161439	0.87[ASN][1000 genomes]
rs11161447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11161465	0.91[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs11161600	0.80[ASN][1000 genomes]
rs11161602	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs11164035	0.87[ASN][1000 genomes]
rs11164037	0.87[ASN][1000 genomes]
rs1144333	0.82[CHB][hapmap]
rs1146648	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1146651	0.81[JPT][hapmap]
rs12022011	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12024645	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs12027620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033058	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12033059	0.82[ASN][1000 genomes]
rs12034697	0.90[ASN][1000 genomes]
rs12044025	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12045299	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs12045363	0.82[ASN][1000 genomes]
rs12076093	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12090712	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12404553	0.90[ASN][1000 genomes]
rs12407107	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs1250876	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1250880	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1251078	0.82[CHB][hapmap]
rs1251079	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs1251272	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs1251274	0.81[CHB][hapmap]
rs12563737	0.81[ASN][1000 genomes]
rs12564772	0.82[ASN][1000 genomes]
rs12728962	0.80[ASN][1000 genomes]
rs12732722	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.96[ASN][1000 genomes]
rs12736447	0.84[ASN][1000 genomes]
rs12744608	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs12747967	0.87[ASN][1000 genomes]
rs12755811	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12756349	0.80[ASN][1000 genomes]
rs1391518	0.87[ASN][1000 genomes]
rs1391520	0.87[ASN][1000 genomes]
rs1535740	0.90[ASN][1000 genomes]
rs1591120	0.90[ASN][1000 genomes]
rs1694428	0.86[JPT][hapmap]
rs17097634	0.82[ASN][1000 genomes]
rs2131558	0.82[ASN][1000 genomes]
rs34486572	0.82[ASN][1000 genomes]
rs35837767	0.87[ASN][1000 genomes]
rs3737574	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs5745314	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs5745334	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs58552356	0.81[ASN][1000 genomes]
rs6665431	0.96[ASN][1000 genomes]
rs6668963	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6676182	0.81[ASN][1000 genomes]
rs6695055	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs67108483	0.87[ASN][1000 genomes]
rs696679	0.82[JPT][hapmap]
rs699683	0.82[JPT][hapmap]
rs699825	0.82[JPT][hapmap]
rs7417486	0.90[ASN][1000 genomes]
rs7514912	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7516477	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7525919	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7548391	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs7548695	0.81[ASN][1000 genomes]
rs7548991	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs815301	0.86[ASN][1000 genomes]
rs815305	0.85[ASN][1000 genomes]
rs9660848	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12745456	MSH4	cis	parietal	SCAN
rs12745456	MSH4	cis	cerebellum	SCAN
rs12745456	ACADM	cis	cerebellum	SCAN
rs12745456	ACADM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76108000-76108200	Enhancers	Esophagus	oesophagus

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