Variant report

Variant	rs12342511
Chromosome Location	chr9:3007331-3007332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10119404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283729	0.87[EUR][1000 genomes]
rs10969468	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10969469	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10969483	0.88[EUR][1000 genomes]
rs10969488	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340058	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59060942	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59086077	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60746952	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385384	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73387545	0.94[EUR][1000 genomes]
rs73387547	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853142	0.87[EUR][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3003400-3008200	Weak transcription	Pancreas	Pancrea
2	chr9:3004200-3007800	Enhancers	Stomach Smooth Muscle	stomach
3	chr9:3004200-3008200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:3005200-3007600	Enhancers	Fetal Muscle Leg	muscle
5	chr9:3005200-3007600	Enhancers	Fetal Stomach	stomach
6	chr9:3005800-3007600	Enhancers	Ovary	ovary
7	chr9:3006400-3007400	Enhancers	Colon Smooth Muscle	Colon
8	chr9:3006400-3007400	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr9:3006400-3007600	Enhancers	Fetal Heart	heart
10	chr9:3006400-3008000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:3006600-3007800	Enhancers	Rectal Smooth Muscle	rectum
12	chr9:3006800-3007800	Enhancers	Stomach Mucosa	stomach
13	chr9:3006800-3008000	Enhancers	Fetal Lung	lung
14	chr9:3007000-3007600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:3007200-3018200	Weak transcription	Fetal Brain Male	brain

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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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