Variant report

Variant	rs12258653
Chromosome Location	chr10:49403264-49403265
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11101250	0.87[AMR][1000 genomes]
rs11101251	1.00[AMR][1000 genomes]
rs11101252	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11101254	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11101270	0.80[YRI][hapmap]
rs11101274	0.89[AMR][1000 genomes]
rs11101276	0.89[AMR][1000 genomes]
rs12241032	0.89[AMR][1000 genomes]
rs12241104	0.89[AMR][1000 genomes]
rs12246849	0.80[YRI][hapmap];0.89[AMR][1000 genomes]
rs12252490	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12252932	0.89[AMR][1000 genomes]
rs12257349	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12257598	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12257690	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17010970	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9651393	0.88[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037726	chr10:49002272-49404608	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv497860	chr10:49002272-49431037	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv831864	chr10:49299274-49450299	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr10:49396000-49420800	Weak transcription	Brain Anterior Caudate	brain
2	chr10:49400800-49403400	Enhancers	Fetal Brain Female	brain
3	chr10:49401200-49404600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr10:49402000-49403600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr10:49402200-49403400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr10:49402200-49403400	Enhancers	HepG2	liver
7	chr10:49402200-49403600	Enhancers	Fetal Intestine Large	intestine
8	chr10:49402200-49404000	Enhancers	Fetal Intestine Small	intestine
9	chr10:49402400-49403400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr10:49402400-49403400	Enhancers	Stomach Mucosa	stomach
11	chr10:49402600-49403400	Enhancers	Duodenum Mucosa	Duodenum
12	chr10:49402600-49403400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr10:49403200-49403600	Enhancers	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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