Variant report

Variant	rs12299228
Chromosome Location	chr12:29387709-29387710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11050133	0.89[EUR][1000 genomes]
rs11050134	1.00[EUR][1000 genomes]
rs11050137	0.89[EUR][1000 genomes]
rs11050138	0.80[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299091	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299148	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307346	0.89[EUR][1000 genomes]
rs12309283	0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309340	0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320498	0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16934037	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766764	1.00[EUR][1000 genomes]
rs7960832	0.90[EUR][1000 genomes]
rs7960834	0.89[EUR][1000 genomes]
rs9804966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804995	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29366200-29393200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29379000-29388000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:29379000-29393400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:29379600-29394600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:29380400-29392000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:29381000-29393200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:29381800-29394600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:29381800-29394800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:29382000-29390000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:29382200-29393400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:29383200-29391600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:29383400-29392000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:29384000-29393200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:29384400-29393200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:29386000-29388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:29386800-29387800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:29386800-29389000	Enhancers	HUVEC	blood vessel
18	chr12:29387600-29388800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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