Variant report

Variant	rs12197514
Chromosome Location	chr6:27553784-27553785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27543936..27547247-chr6:27553290..27555212,3	K562	blood:
2	chr6:27549818..27556949-chr6:27557615..27563432,7	K562	blood:
3	chr6:27515165..27518892-chr6:27550748..27553909,3	K562	blood:
4	chr6:27549715..27554180-chr6:27555593..27563261,8	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1022486	0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10807026	0.87[ASN][1000 genomes]
rs10946935	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10946938	0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946940	0.89[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2056924	0.87[JPT][hapmap]
rs2294480	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2294481	0.95[JPT][hapmap]
rs4272217	0.84[ASN][1000 genomes]
rs4713112	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4713113	0.87[ASN][1000 genomes]
rs4713120	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs62401383	0.82[ASN][1000 genomes]
rs6456799	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs67734963	0.81[ASN][1000 genomes]
rs6908295	0.82[ASN][1000 genomes]
rs6915266	0.85[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6915987	0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs6916878	0.86[JPT][hapmap]
rs6921256	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs6933926	0.81[ASN][1000 genomes]
rs6934437	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6934794	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7764081	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7774939	0.87[ASN][1000 genomes]
rs7775817	0.88[ASN][1000 genomes]
rs9295747	0.82[JPT][hapmap]
rs9348772	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs9380007	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs9393830	0.84[JPT][hapmap]
rs9393831	0.85[CHD][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12197514	ZNF204P	cis	parietal	SCAN
rs12197514	BTN3A3	cis	cerebellum	SCAN
rs12197514	ZNF391	cis	cerebellum	SCAN
rs12197514	ZKSCAN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27551400-27556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:27551400-27559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:27552200-27559200	Weak transcription	A549	lung
4	chr6:27553600-27553800	Flanking Active TSS	K562	blood
5	chr6:27553600-27555200	Enhancers	HepG2	liver

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