Variant report

Variant	rs12346629
Chromosome Location	chr9:3040340-3040341
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10124397	1.00[EUR][1000 genomes]
rs12336010	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12350114	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12350982	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2327708	1.00[EUR][1000 genomes]
rs3847246	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3895474	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56795760	1.00[EUR][1000 genomes]
rs57265062	1.00[EUR][1000 genomes]
rs60499116	1.00[EUR][1000 genomes]
rs60722825	1.00[EUR][1000 genomes]
rs60931896	1.00[EUR][1000 genomes]
rs73389564	1.00[EUR][1000 genomes]
rs73389579	1.00[EUR][1000 genomes]
rs73389582	1.00[EUR][1000 genomes]
rs73639934	1.00[EUR][1000 genomes]
rs7857284	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9785200	1.00[EUR][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	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016036	chr9:3003995-3054185	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv831494	chr9:3007268-3172056	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv892087	chr9:3014702-3153178	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv892088	chr9:3019383-3215842	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1025022	chr9:3024191-3074498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3351385	chr9:3038702-3041100	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	esv3403751	chr9:3039202-3040700	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3032800-3042200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:3039600-3040400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:3040200-3040600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:3040200-3041600	Enhancers	Muscle Satellite Cultured Cells	--

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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

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