Variant report

Variant	rs12200540
Chromosome Location	chr6:4983763-4983764
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4976929..4979800-chr6:4982813..4985297,2	K562	blood:
2	chr6:4983378..4985283-chr6:4997701..4999628,2	K562	blood:
3	chr6:4980056..4981977-chr6:4983489..4985238,2	K562	blood:
4	chr6:4983698..4989646-chr6:5001005..5005848,7	K562	blood:
5	chr6:4983698..4985675-chr6:5003583..5005598,3	K562	blood:
6	chr6:4983360..4985450-chr6:5029648..5031623,2	K562	blood:
7	chr6:4976929..4979884-chr6:4982508..4985297,3	K562	blood:
8	chr6:4982368..4985908-chr6:4994564..4997355,3	K562	blood:
9	chr6:4982550..4985450-chr6:5030123..5032818,2	K562	blood:
10	chr6:4978280..4980580-chr6:4983481..4985343,2	MCF-7	breast:
11	chr6:4980477..4982154-chr6:4983447..4984989,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10458082	0.96[EUR][1000 genomes]
rs10458083	0.96[EUR][1000 genomes]
rs10458181	0.96[EUR][1000 genomes]
rs12191838	1.00[EUR][1000 genomes]
rs12196163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12197502	0.96[EUR][1000 genomes]
rs12200807	0.84[EUR][1000 genomes]
rs12201300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12208967	0.88[EUR][1000 genomes]
rs12212086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12212682	0.96[EUR][1000 genomes]
rs12212751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12214401	1.00[EUR][1000 genomes]
rs1246984	0.86[EUR][1000 genomes]
rs9392644	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4979600-4985400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:4980400-4989800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:4981600-4984200	Enhancers	HepG2	liver
4	chr6:4982000-4985200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr6:4982400-4985200	Weak transcription	Right Atrium	heart
6	chr6:4982400-4995000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:4982600-4984400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:4982600-4991000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:4982600-4995000	Weak transcription	Fetal Thymus	thymus
10	chr6:4983000-4985200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:4983000-4997600	Weak transcription	Psoas Muscle	Psoas
12	chr6:4983600-4984200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:4983600-4988800	Enhancers	K562	blood

Quick Search:

Input of quick search could be:

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

what's new

Quick links