Variant report

Variant	rs9379960
Chromosome Location	chr6:27121325-27121326
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27119707..27122211-chr6:27833105..27834981,2	K562	blood:
2	chr6:27120905..27123072-chr6:27791048..27793048,2	K562	blood:
3	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
4	chr6:27119654..27121827-chr6:27782720..27784268,2	MCF-7	breast:
5	chr6:27120589..27123058-chr6:27135123..27137850,2	MCF-7	breast:
6	chr6:27117733..27121878-chr6:27773539..27777847,4	MCF-7	breast:
7	chr6:27121049..27122918-chr6:27780624..27782591,2	K562	blood:
8	chr6:27119142..27122211-chr6:27832500..27834981,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198374	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000182611	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1028308	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];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946899	0.83[CEU][hapmap]
rs11756275	0.85[JPT][hapmap]
rs12527111	0.85[JPT][hapmap]
rs2022272	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2142685	0.85[JPT][hapmap]
rs2393915	0.85[JPT][hapmap]
rs2393918	0.80[JPT][hapmap]
rs4582379	0.80[JPT][hapmap]
rs4713069	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6456766	0.89[EUR][1000 genomes]
rs6456767	0.85[JPT][hapmap]
rs6456768	0.85[JPT][hapmap]
rs6921388	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925226	0.92[EUR][1000 genomes]
rs6930508	0.85[JPT][hapmap]
rs7744759	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7745603	0.80[TSI][hapmap]
rs7747454	0.85[JPT][hapmap]
rs7764984	0.88[EUR][1000 genomes]
rs858964	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295730	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348750	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9348751	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461335	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994691	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9379960	ZKSCAN3	cis	parietal	SCAN
rs9379960	HIST1H2BM	cis	cerebellum	SCAN
rs9379960	BTN2A1	cis	parietal	SCAN
rs9379960	BTN3A3	cis	parietal	SCAN
rs9379960	BTN3A2	cis	lymphoblastoid	seeQTL
rs9379960	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9379960	HIST1H2BH	cis	cerebellum	SCAN
rs9379960	BTN3A2	cis	cerebellum	SCAN
rs9379960	BTN3A3	cis	cerebellum	SCAN
rs9379960	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27115600-27124800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:27115600-27125000	Weak transcription	Right Atrium	heart
3	chr6:27116000-27123000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:27116200-27122600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:27117200-27122200	Weak transcription	GM12878-XiMat	blood
6	chr6:27117200-27122800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:27117200-27124800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:27117400-27122000	Weak transcription	Dnd41	blood
9	chr6:27117400-27122600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:27117400-27122800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:27117400-27123000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:27118600-27122800	Weak transcription	K562	blood
13	chr6:27120600-27122000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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