Variant report

Variant	rs9353324
Chromosome Location	chr6:86362874-86362875
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86360455..86373602-chr6:86382637..86391992,19	MCF-7	breast:
2	chr6:86350940..86355253-chr6:86359702..86365737,10	K562	blood:
3	chr6:86299850..86302872-chr6:86358961..86362964,3	K562	blood:

Variant related genes	Relation type
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12524836	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12528808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12664908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229524	0.95[EUR][1000 genomes]
rs3812137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap]
rs3812139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4327657	0.95[EUR][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4400191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs59744370	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs6902638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs6906618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6910543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6913634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.95[EUR][1000 genomes]
rs6923017	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930543	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7744309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7745560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7749600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7752105	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7757466	0.83[AFR][1000 genomes]
rs7760309	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7766284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7771366	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7775016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs7775788	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9344530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9344538	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9351063	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9351066	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9353319	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9353321	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9353323	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9359656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362225	0.95[EUR][1000 genomes]
rs9362226	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9444353	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9444356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450286	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap]
rs9450289	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450294	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450295	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450299	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9450300	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9450304	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450309	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
5	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9353324	NT5E	cis	lymphoblastoid	seeQTL
rs9353324	C6orf160	cis	multi-tissue	Pritchard
rs9353324	NT5E	cis	Thyroid	GTEx
rs9353324	NT5E	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354200-86374400	Weak transcription	Left Ventricle	heart
2	chr6:86354600-86369600	Weak transcription	Ovary	ovary
3	chr6:86354600-86372200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:86355200-86369800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:86355200-86377000	Weak transcription	Thymus	Thymus
7	chr6:86355200-86380400	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
9	chr6:86355600-86369600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:86360000-86369800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:86360600-86375000	Weak transcription	Brain Germinal Matrix	brain

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