Variant report

Variant	rs9394580
Chromosome Location	chr6:39243842-39243843
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39196978..39198993-chr6:39243328..39246194,3	K562	blood:
2	chr6:39240523..39244812-chr6:39255962..39259170,3	MCF-7	breast:
3	chr6:39243650..39250520-chr6:39262135..39271800,15	MCF-7	breast:
4	chr6:39196646..39198623-chr6:39241718..39244423,2	MCF-7	breast:
5	chr6:39238194..39240550-chr6:39241911..39243898,2	K562	blood:
6	chr6:39242418..39244408-chr6:39246030..39248375,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1005995	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1182864	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12191604	0.89[ASN][1000 genomes]
rs12191756	0.89[ASN][1000 genomes]
rs12198547	0.81[ASN][1000 genomes]
rs12202277	0.83[AFR][1000 genomes]
rs12202455	0.83[AFR][1000 genomes]
rs2253582	0.90[ASN][1000 genomes]
rs2395719	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395720	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2758864	0.89[ASN][1000 genomes]
rs2758865	0.88[ASN][1000 genomes]
rs2758866	0.89[ASN][1000 genomes]
rs2758867	0.89[ASN][1000 genomes]
rs2758868	0.88[ASN][1000 genomes]
rs2758869	0.89[ASN][1000 genomes]
rs2758871	0.93[ASN][1000 genomes]
rs2758872	0.93[ASN][1000 genomes]
rs2758874	0.93[ASN][1000 genomes]
rs2815019	0.89[ASN][1000 genomes]
rs2815020	0.91[ASN][1000 genomes]
rs2815024	0.89[ASN][1000 genomes]
rs2815025	0.89[ASN][1000 genomes]
rs2815026	0.89[ASN][1000 genomes]
rs2815027	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2815028	0.89[ASN][1000 genomes]
rs2815029	0.89[ASN][1000 genomes]
rs2815030	0.95[ASN][1000 genomes]
rs2815031	0.89[ASN][1000 genomes]
rs2815032	0.90[ASN][1000 genomes]
rs2815035	0.90[ASN][1000 genomes]
rs2815036	0.90[ASN][1000 genomes]
rs2815037	0.90[ASN][1000 genomes]
rs2815038	0.90[ASN][1000 genomes]
rs2815039	0.93[ASN][1000 genomes]
rs2815040	0.93[ASN][1000 genomes]
rs2815041	0.93[ASN][1000 genomes]
rs2815042	0.92[ASN][1000 genomes]
rs2815044	0.93[ASN][1000 genomes]
rs2815045	0.89[ASN][1000 genomes]
rs2815061	0.89[ASN][1000 genomes]
rs34170020	0.86[ASN][1000 genomes]
rs34343201	0.86[ASN][1000 genomes]
rs4711593	0.87[AFR][1000 genomes]
rs4714233	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746595	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39240400-39250200	Enhancers	Stomach Mucosa	stomach
2	chr6:39242000-39247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:39242000-39247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:39242600-39247200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:39242600-39249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:39243000-39245800	Weak transcription	Placenta	Placenta
7	chr6:39243200-39247200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr6:39243600-39244200	Enhancers	Colonic Mucosa	Colon
9	chr6:39243600-39247000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:39243600-39247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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