Variant report

Variant	rs9390009
Chromosome Location	chr6:142927252-142927253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142925129..142927801-chr6:142932639..142935084,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1070576	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1070577	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1098067	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1098071	0.85[ASN][1000 genomes]
rs13217677	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1417359	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs171913	0.83[ASN][1000 genomes]
rs171914	0.83[ASN][1000 genomes]
rs263114	0.85[ASN][1000 genomes]
rs263120	0.91[ASN][1000 genomes]
rs263121	0.91[ASN][1000 genomes]
rs263154	0.95[ASN][1000 genomes]
rs263166	0.88[ASN][1000 genomes]
rs263175	0.82[ASN][1000 genomes]
rs2664050	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28514730	0.80[EUR][1000 genomes]
rs35670034	0.82[EUR][1000 genomes]
rs35781078	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56077882	0.87[EUR][1000 genomes]
rs67446783	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6906209	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916595	0.82[EUR][1000 genomes]
rs6917687	0.82[EUR][1000 genomes]
rs6921853	0.93[EUR][1000 genomes]
rs6939573	0.82[EUR][1000 genomes]
rs702289	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs702290	0.82[ASN][1000 genomes]
rs702291	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs702292	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs702293	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs702294	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs702295	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702296	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs702298	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759020	0.82[EUR][1000 genomes]
rs844443	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863432	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9321872	0.91[AFR][1000 genomes]
rs9386003	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9390007	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390011	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403400	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9496420	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9496423	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9496425	0.82[EUR][1000 genomes]
rs9496427	0.93[EUR][1000 genomes]
rs9496428	0.82[EUR][1000 genomes]
rs9496429	0.82[EUR][1000 genomes]
rs9496432	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9496434	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142925200-142928000	Enhancers	Primary T cells from cord blood	blood
2	chr6:142926800-142927400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:142926800-142927600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:142926800-142927800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:142926800-142927800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:142927000-142927600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:142927000-142927600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr6:142927000-142927600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:142927000-142927600	Enhancers	NHEK	skin
10	chr6:142927000-142927800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:142927000-142928000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:142927000-142928000	Flanking Active TSS	Osteobl	bone
13	chr6:142927200-142927400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:142927200-142927400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:142927200-142927400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr6:142927200-142927600	Flanking Active TSS	NH-A	brain

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