Variant report

Variant	rs28407876
Chromosome Location	chr4:9765165-9765166
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:91815162..91820044-chr4:9763391..9768700,25	MCF-7	breast:
2	chr1:149221736..149225365-chr4:9763717..9766826,4	MCF-7	breast:
3	chr2:91815178..91817122-chr4:9765055..9766792,2	K562	blood:
4	chr2:91815622..91818416-chr4:9765055..9766802,2	K562	blood:
5	chr4:9764445..9765327-chr4:10020033..10020988,3	K562	blood:
6	chr4:9764437..9765430-chr4:10020023..10020916,6	MCF-7	breast:
7	chr2:91818675..91820415-chr4:9765033..9768552,3	K562	blood:
8	chr4:9764370..9765339-chr4:10015197..10016013,4	MCF-7	breast:
9	chr4:9763456..9766236-chr4:10014004..10016919,3	K562	blood:
10	chr2:91816088..91820118-chr4:9765029..9767622,10	MCF-7	breast:
11	chr4:9764866..9765415-chr4:9928949..9929492,2	MCF-7	breast:
12	chr4:9764793..9765717-chr4:10015113..10016017,3	MCF-7	breast:
13	chr2:91816303..91817383-chr4:9764391..9765414,6	MCF-7	breast:
14	chr4:9764792..9765537-chr4:9899989..9900954,5	MCF-7	breast:
15	chr2:91816443..91817305-chr4:9764390..9765414,6	MCF-7	breast:
16	chr1:149220703..149225113-chr4:9764948..9767069,4	MCF-7	breast:
17	chr4:9764428..9765300-chr4:10016550..10017565,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12640694	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648522	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16888725	0.83[AFR][1000 genomes]
rs16888799	0.83[AFR][1000 genomes]
rs1850740	0.83[AFR][1000 genomes]
rs2030287	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28372608	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28413933	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28523967	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28528381	0.83[AFR][1000 genomes]
rs28589531	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2867382	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56095448	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56249678	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62293224	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6449009	0.81[EUR][1000 genomes]
rs6812531	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	esv2754610	chr4:9372303-9804524	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
4	nsv1012865	chr4:9429299-9794181	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1001143	chr4:9435322-9794181	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1012621	chr4:9456977-9802366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1012634	chr4:9461218-9802366	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv998043	chr4:9496282-9830208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
9	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv878669	chr4:9551094-9794724	Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv999102	chr4:9633247-9794181	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
13	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 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	chr4:9755800-9766200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:9760400-9766200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:9763600-9767600	Weak transcription	Right Atrium	heart
4	chr4:9764400-9765200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr4:9764600-9765200	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr4:9764600-9765200	Enhancers	Fetal Stomach	stomach
7	chr4:9764600-9765200	Enhancers	Fetal Thymus	thymus
8	chr4:9764600-9765200	Enhancers	HepG2	liver
9	chr4:9764600-9765400	Enhancers	Fetal Muscle Leg	muscle
10	chr4:9765000-9765200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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