Variant report

Variant	rs12079449
Chromosome Location	chr1:120404936-120404937
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10158823	1.00[YRI][hapmap]
rs10923908	0.89[YRI][hapmap]
rs10923913	0.99[AFR][1000 genomes]
rs10923915	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10923922	0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12059465	0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12082526	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097726	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1341408	0.80[AFR][1000 genomes]
rs17024340	0.84[YRI][hapmap]
rs17024398	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17038441	1.00[YRI][hapmap]
rs3850867	0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6666925	1.00[YRI][hapmap]
rs7354885	0.84[YRI][hapmap];0.89[AMR][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv872180	chr1:120366055-120412885	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv946187	chr1:120370078-120406007	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv10672	chr1:120386985-120410007	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120400800-120405000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:120401400-120415000	Weak transcription	Fetal Kidney	kidney
3	chr1:120402400-120410800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:120402800-120413800	Weak transcription	HSMMtube	muscle
5	chr1:120403400-120405000	Enhancers	Fetal Intestine Large	intestine
6	chr1:120403600-120405200	Enhancers	NHDF-Ad	bronchial
7	chr1:120403800-120409200	Weak transcription	K562	blood
8	chr1:120404000-120413600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:120404200-120413800	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:120404400-120405600	Enhancers	NHLF	lung
11	chr1:120404400-120408000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:120404800-120405000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:120404800-120405000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:120404800-120405000	Enhancers	NH-A	brain
15	chr1:120404800-120406800	Weak transcription	Stomach Mucosa	stomach

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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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