Variant report

Variant	rs9397070
Chromosome Location	chr6:150243209-150243210
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	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
2	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164520	Chromatin interaction
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10457852	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12204653	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12209310	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12210822	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12527391	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12528243	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1855572	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1999632	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2342766	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3798763	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3922946	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3922947	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4473864	0.82[ASN][1000 genomes]
rs4869755	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4869756	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4869767	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4869768	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4870078	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4870110	0.82[ASN][1000 genomes]
rs4870117	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4870118	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024811	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57894361	0.81[EUR][1000 genomes]
rs6557165	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6912330	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6925151	0.92[EUR][1000 genomes]
rs7452592	0.82[EUR][1000 genomes]
rs7764677	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs915140	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9322229	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9371228	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9383941	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9397070	RP11-350J20.5	cis	lung	GTEx
rs9397070	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9397070	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9397070	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150227800-150243400	Weak transcription	Right Ventricle	heart
2	chr6:150230400-150243600	Weak transcription	Pancreas	Pancrea
3	chr6:150237200-150243600	Weak transcription	Right Atrium	heart
4	chr6:150239600-150243400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:150239600-150243400	Weak transcription	NHEK	skin
6	chr6:150239800-150243400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:150239800-150243400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:150239800-150243600	Weak transcription	Esophagus	oesophagus
9	chr6:150241200-150243800	Weak transcription	Aorta	Aorta
10	chr6:150242400-150243800	Enhancers	Spleen	Spleen
11	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:150243000-150243400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:150243000-150243800	Bivalent Enhancer	Fetal Intestine Large	intestine
14	chr6:150243000-150243800	Weak transcription	Gastric	stomach
15	chr6:150243200-150243400	Enhancers	HMEC	breast
16	chr6:150243200-150243600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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