Variant report

Variant	rs9461362
Chromosome Location	chr6:27303927-27303928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27303156..27306028-chr6:27355020..27356992,2	MCF-7	breast:
2	chr6:27154842..27156986-chr6:27301919..27304257,2	K562	blood:

Variant related genes	Relation type
ENSG00000124613	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1127574	0.81[ASN][1000 genomes]
rs12199213	0.81[ASN][1000 genomes]
rs12213055	1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs1555040	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs17687635	1.00[CEU][hapmap]
rs17688516	1.00[JPT][hapmap]
rs17739298	0.81[CEU][hapmap]
rs17739310	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap]
rs17739702	1.00[JPT][hapmap]
rs17739727	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs4145206	0.81[CEU][hapmap];0.84[CHD][hapmap]
rs55923531	0.88[ASN][1000 genomes]
rs56388125	1.00[ASN][1000 genomes]
rs721600	0.82[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs764285	0.83[ASN][1000 genomes]
rs9348760	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9348761	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9348762	0.87[AFR][1000 genomes]
rs9368502	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9379976	0.86[ASW][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs9379977	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap]
rs9379978	0.86[ASW][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9393807	1.00[YRI][hapmap]
rs9393808	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9461355	1.00[CEU][hapmap]
rs9461357	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[MEX][hapmap]
rs9461358	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9461359	0.83[AFR][1000 genomes]
rs9461360	0.83[AFR][1000 genomes]
rs9461363	0.86[ASN][1000 genomes]
rs9461366	0.83[ASN][1000 genomes]
rs9468047	0.82[YRI][hapmap]
rs9468067	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap]
rs9468068	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs9468069	0.83[AFR][1000 genomes]
rs9468076	0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs9468149	0.89[JPT][hapmap]
rs9468152	0.89[JPT][hapmap]
rs9468153	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2761047	chr6:27296775-27303927	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9461362	FER1L6	trans	parietal	SCAN
rs9461362	ZNF192	cis	parietal	SCAN
rs9461362	HIST1H2AL	cis	cerebellum	SCAN
rs9461362	ZNF204P	cis	cerebellum	SCAN
rs9461362	HIST1H4F	cis	cerebellum	SCAN
rs9461362	ZSCAN12	cis	parietal	SCAN
rs9461362	HIST1H4B	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27301400-27321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:27302400-27304600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:27303000-27304200	Weak transcription	HepG2	liver
4	chr6:27303200-27304200	Weak transcription	K562	blood

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