Variant report

Variant	rs28780081
Chromosome Location	chr6:30064015-30064016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30058600..30061539-chr6:30062741..30064895,3	MCF-7	breast:
2	chr6:30058142..30060356-chr6:30062997..30064640,2	MCF-7	breast:
3	chr6:30040732..30043488-chr6:30062276..30064354,2	K562	blood:
4	chr6:30036068..30037732-chr6:30063349..30066200,2	MCF-7	breast:
5	chr6:30033726..30035867-chr6:30063166..30065210,2	MCF-7	breast:
6	chr6:30041901..30046365-chr6:30059553..30065121,9	MCF-7	breast:
7	chr6:30039555..30048654-chr6:30056865..30065735,15	MCF-7	breast:
8	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
9	chr6:30053423..30056076-chr6:30062128..30065252,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204619	Chromatin interaction
ENSG00000204618	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1108052	0.87[ASN][1000 genomes]
rs1108053	0.91[ASN][1000 genomes]
rs1110448	0.91[ASN][1000 genomes]
rs1156533	0.86[ASN][1000 genomes]
rs11751554	0.83[ASN][1000 genomes]
rs11755853	0.80[AFR][1000 genomes]
rs11967911	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11968367	0.83[ASN][1000 genomes]
rs11968434	0.83[ASN][1000 genomes]
rs1264694	0.90[ASN][1000 genomes]
rs1264695	0.91[ASN][1000 genomes]
rs1264696	0.91[ASN][1000 genomes]
rs1264702	0.93[ASN][1000 genomes]
rs12661731	0.86[ASN][1000 genomes]
rs17187791	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17187805	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17194146	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17194153	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17194160	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17194174	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072110	0.88[ASN][1000 genomes]
rs2523994	0.88[ASN][1000 genomes]
rs28454792	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28780078	0.86[ASN][1000 genomes]
rs28780079	0.86[ASN][1000 genomes]
rs28780080	0.86[ASN][1000 genomes]
rs28780082	0.85[ASN][1000 genomes]
rs57195817	0.85[ASN][1000 genomes]
rs60418878	0.81[ASN][1000 genomes]
rs61666432	0.83[ASN][1000 genomes]
rs6457149	0.92[ASN][1000 genomes]
rs73424274	0.81[ASN][1000 genomes]
rs7741418	0.86[ASN][1000 genomes]
rs7749793	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753935	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7754005	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7761563	0.86[ASN][1000 genomes]
rs7765810	0.86[ASN][1000 genomes]
rs7771071	0.83[ASN][1000 genomes]
rs916569	0.91[ASN][1000 genomes]
rs916570	0.91[ASN][1000 genomes]
rs9261384	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30060000-30064800	Weak transcription	Gastric	stomach
2	chr6:30060200-30065600	Weak transcription	Spleen	Spleen
3	chr6:30060400-30065200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:30061000-30066800	Enhancers	Stomach Mucosa	stomach
5	chr6:30062000-30067000	Enhancers	Fetal Intestine Small	intestine
6	chr6:30062200-30067800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:30062600-30064800	Enhancers	Fetal Intestine Large	intestine
8	chr6:30063400-30068400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:30063600-30065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30063600-30068200	Weak transcription	HMEC	breast
11	chr6:30063800-30064800	Weak transcription	K562	blood
12	chr6:30063800-30065400	Weak transcription	NHEK	skin
13	chr6:30063800-30068000	Weak transcription	Lung	lung
14	chr6:30064000-30068000	Enhancers	HepG2	liver

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