Variant report

Variant	rs12645107
Chromosome Location	chr4:69988999-69989000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs12152625	0.83[MEX][hapmap]
rs12640790	0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12646304	0.83[EUR][1000 genomes]
rs12647599	0.83[EUR][1000 genomes]
rs12648462	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649866	0.83[EUR][1000 genomes]
rs12650658	0.83[EUR][1000 genomes]
rs35151589	0.83[EUR][1000 genomes]
rs35264089	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4309909	0.83[EUR][1000 genomes]
rs4326076	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4326077	0.83[EUR][1000 genomes]
rs4377651	0.84[MEX][hapmap];0.89[TSI][hapmap]
rs4438816	0.89[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4472206	0.83[EUR][1000 genomes]
rs4479775	0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs4479776	0.80[EUR][1000 genomes]
rs4593202	0.83[EUR][1000 genomes]
rs4593203	0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4604120	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4611998	0.83[EUR][1000 genomes]
rs4615240	0.83[EUR][1000 genomes]
rs55762706	0.81[EUR][1000 genomes]
rs56016159	0.82[EUR][1000 genomes]
rs57025126	0.81[EUR][1000 genomes]
rs57226662	0.82[EUR][1000 genomes]
rs57244408	0.81[EUR][1000 genomes]
rs57449680	0.83[EUR][1000 genomes]
rs57955338	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58042229	0.83[EUR][1000 genomes]
rs58077880	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58174838	0.89[EUR][1000 genomes]
rs58655780	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58826998	0.83[EUR][1000 genomes]
rs58878867	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59514779	0.82[EUR][1000 genomes]
rs59704026	0.82[EUR][1000 genomes]
rs59970425	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59983350	0.83[EUR][1000 genomes]
rs60162445	0.83[EUR][1000 genomes]
rs60749735	0.83[EUR][1000 genomes]
rs61137241	0.81[EUR][1000 genomes]
rs61162302	0.88[EUR][1000 genomes]
rs61174505	0.88[EUR][1000 genomes]
rs61220696	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61281368	0.83[EUR][1000 genomes]
rs61658486	0.83[EUR][1000 genomes]
rs6818992	0.86[EUR][1000 genomes]
rs6823903	0.89[MEX][hapmap]
rs6833862	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs6838793	0.83[EUR][1000 genomes]
rs6857759	0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs72851317	0.88[EUR][1000 genomes]
rs72851318	0.87[EUR][1000 genomes]
rs72851322	0.87[EUR][1000 genomes]
rs72851362	0.89[EUR][1000 genomes]
rs72851371	0.84[EUR][1000 genomes]
rs72851378	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72851379	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72852429	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72852498	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72853561	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72853597	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72855408	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72855411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72855460	0.83[EUR][1000 genomes]
rs72855468	0.83[EUR][1000 genomes]
rs72855469	0.83[EUR][1000 genomes]
rs72855471	0.83[EUR][1000 genomes]
rs72855482	0.84[EUR][1000 genomes]
rs73823891	0.83[EUR][1000 genomes]
rs73823894	0.83[EUR][1000 genomes]
rs73826069	0.88[EUR][1000 genomes]
rs7438042	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7442353	0.81[CHB][hapmap]
rs7660744	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7666267	0.81[EUR][1000 genomes]
rs7671480	0.89[MEX][hapmap];0.96[TSI][hapmap]
rs7674201	0.83[EUR][1000 genomes]
rs7677390	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7685017	0.83[EUR][1000 genomes]
rs7685409	0.83[EUR][1000 genomes]
rs7698243	0.82[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427683	chr4:69929701-70414172	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv999858	chr4:69933262-70676525	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1000261	chr4:69954600-70642254	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv537134	chr4:69954600-70642254	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv879380	chr4:69961912-70046930	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv879381	chr4:69972086-70046930	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv879382	chr4:69972086-70066719	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv1806087	chr4:69975196-70276308	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12645107	STATH	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69981600-69990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:69986400-69989800	Weak transcription	NHEK	skin
3	chr4:69987800-69990600	Weak transcription	Gastric	stomach
4	chr4:69988200-69989400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:69988800-69989800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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