Variant report

Variant	rs9396006
Chromosome Location	chr6:54787888-54787889
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	chr6:54710888..54713674-chr6:54785634..54788254,2	MCF-7	breast:
2	chr6:54787385..54788945-chr6:54793642..54795973,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10485136	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1115159	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12525787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662124	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393776	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs148109	0.85[JPT][hapmap]
rs1503140	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1503146	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1503147	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1963697	0.81[CEU][hapmap]
rs2064432	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816811	0.85[JPT][hapmap]
rs4141552	0.94[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4712081	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715491	0.83[CEU][hapmap]
rs6459035	0.93[EUR][1000 genomes]
rs6902245	0.84[EUR][1000 genomes]
rs6902422	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6908170	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922186	0.84[EUR][1000 genomes]
rs6926997	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6929930	0.84[EUR][1000 genomes]
rs6939778	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72645372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7453866	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7739399	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7744592	0.83[EUR][1000 genomes]
rs7746374	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296771	0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932452	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9349740	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs9357840	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs9367597	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367602	0.92[ASN][1000 genomes]
rs9370332	0.93[JPT][hapmap]
rs9370333	0.93[JPT][hapmap]
rs9370337	0.80[ASN][1000 genomes]
rs9370344	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370345	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs9370350	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9370351	0.92[ASN][1000 genomes]
rs9370352	0.92[ASN][1000 genomes]
rs9382396	0.91[EUR][1000 genomes]
rs9382397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382402	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9382403	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs9382411	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9396007	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9396013	0.91[ASN][1000 genomes]
rs9396036	0.85[CHB][hapmap]
rs9475068	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475069	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9475078	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9475081	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475106	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475107	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs960834	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs960835	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs988913	0.89[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54775600-54788400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:54776000-54796800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:54781800-54796800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:54782200-54791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54782200-54792200	Weak transcription	NHEK	skin
6	chr6:54782200-54792400	Weak transcription	HMEC	breast
7	chr6:54782200-54792600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:54785600-54805000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:54786200-54788200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:54786600-54790000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:54786800-54800000	Weak transcription	Hela-S3	cervix

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