Variant report

Variant	rs9348761
Chromosome Location	chr6:27302825-27302826
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27218055..27220276-chr6:27300325..27303096,3	K562	blood:
2	chr6:27298779..27303006-chr6:27440534..27442735,4	K562	blood:
3	chr6:27298898..27303175-chr6:27340830..27343404,5	K562	blood:
4	chr6:27154842..27156986-chr6:27301919..27304257,2	K562	blood:
5	chr6:27300837..27303680-chr6:27307517..27309958,2	K562	blood:
6	chr6:27276791..27280576-chr6:27298923..27302888,5	K562	blood:

Variant related genes	Relation type
ENSG00000158553	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000112812	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1127574	0.84[EUR][1000 genomes]
rs12199213	0.84[EUR][1000 genomes]
rs12213055	0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs17739727	0.94[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs721600	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9368502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379976	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9379978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393805	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393806	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393807	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9393808	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461359	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461360	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461362	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]
rs9468047	0.82[YRI][hapmap]
rs9468068	1.00[YRI][hapmap]
rs9468069	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468076	0.94[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9348761	ZNF391	cis	cerebellum	SCAN
rs9348761	ZNF204P	cis	cerebellum	SCAN
rs9348761	BTN3A3	cis	cerebellum	SCAN
rs9348761	HIST1H2AL	cis	cerebellum	SCAN
rs9348761	HIST1H4B	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27300200-27303200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27300200-27303400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27300400-27303200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:27300400-27303200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:27300400-27303400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:27300400-27303600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:27301400-27321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:27302400-27303000	Active TSS	NHEK	skin
9	chr6:27302400-27303200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:27302400-27303200	Active TSS	K562	blood
11	chr6:27302400-27304600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:27302800-27303000	Enhancers	HepG2	liver

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