Variant report

Variant	rs28780078
Chromosome Location	chr6:30062650-30062651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30034665..30036494-chr6:30061234..30063128,2	MCF-7	breast:
2	chr6:30040732..30043488-chr6:30062276..30064354,2	K562	blood:
3	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
4	chr6:30041901..30046365-chr6:30059553..30065121,9	MCF-7	breast:
5	chr6:30039555..30048654-chr6:30056865..30065735,15	MCF-7	breast:
6	chr6:30039304..30041261-chr6:30060958..30063803,2	MCF-7	breast:
7	chr6:30053423..30056076-chr6:30062128..30065252,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204618	Chromatin interaction
ENSG00000204619	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1108052	0.88[ASN][1000 genomes]
rs1108053	0.91[ASN][1000 genomes]
rs1110448	0.91[ASN][1000 genomes]
rs1156533	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11751554	0.82[ASN][1000 genomes]
rs11967911	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11968367	0.82[ASN][1000 genomes]
rs11968434	0.82[ASN][1000 genomes]
rs1264694	0.84[ASN][1000 genomes]
rs1264695	0.91[ASN][1000 genomes]
rs1264696	0.91[ASN][1000 genomes]
rs1264702	0.93[ASN][1000 genomes]
rs12661731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17187791	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17187805	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17194146	0.85[ASN][1000 genomes]
rs17194153	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17194160	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17194174	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2072110	0.89[ASN][1000 genomes]
rs2523994	0.89[ASN][1000 genomes]
rs28454792	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28780079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780081	0.86[ASN][1000 genomes]
rs28780082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60418878	0.81[ASN][1000 genomes]
rs61666432	0.82[ASN][1000 genomes]
rs6457149	0.90[ASN][1000 genomes]
rs73424274	0.81[ASN][1000 genomes]
rs7741418	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749793	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7753935	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7754005	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7761563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771071	0.82[ASN][1000 genomes]
rs916569	0.91[ASN][1000 genomes]
rs916570	0.91[ASN][1000 genomes]
rs9261384	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884052	chr6:30059592-30067681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
6	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30060000-30063000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:30060000-30063000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:30060000-30063000	Weak transcription	A549	lung
4	chr6:30060000-30064800	Weak transcription	Gastric	stomach
5	chr6:30060200-30063000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:30060200-30063000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:30060200-30063000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:30060200-30063000	Weak transcription	NHEK	skin
9	chr6:30060200-30063200	Weak transcription	HMEC	breast
10	chr6:30060200-30065600	Weak transcription	Spleen	Spleen
11	chr6:30060400-30063000	Weak transcription	Hela-S3	cervix
12	chr6:30060400-30065200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:30061000-30066800	Enhancers	Stomach Mucosa	stomach
14	chr6:30062000-30063800	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:30062000-30067000	Enhancers	Fetal Intestine Small	intestine
16	chr6:30062200-30067800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:30062400-30063000	Enhancers	HepG2	liver
18	chr6:30062600-30064800	Enhancers	Fetal Intestine Large	intestine

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