Variant report

Variant	rs297904
Chromosome Location	chr12:50310193-50310194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17119741	1.00[EUR][1000 genomes]
rs2232209	1.00[EUR][1000 genomes]
rs297903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs297908	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs297912	1.00[EUR][1000 genomes]
rs297915	1.00[EUR][1000 genomes]
rs364895	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs394682	1.00[ASW][hapmap]
rs408045	1.00[MEX][hapmap]
rs440721	1.00[EUR][1000 genomes]
rs487193	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55853170	1.00[EUR][1000 genomes]
rs57423894	1.00[EUR][1000 genomes]
rs7304815	1.00[EUR][1000 genomes]
rs74089213	1.00[EUR][1000 genomes]
rs74091125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv558836	chr12:50290023-50316439	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50303400-50311800	Weak transcription	Gastric	stomach
2	chr12:50304200-50319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:50304600-50314600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:50308400-50310800	Weak transcription	Fetal Brain Female	brain
5	chr12:50308400-50311200	Weak transcription	Brain Germinal Matrix	brain
6	chr12:50308600-50311000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:50308600-50313400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:50308600-50314000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:50308600-50314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:50308600-50314600	Weak transcription	Right Atrium	heart
11	chr12:50309600-50311200	Enhancers	Hela-S3	cervix
12	chr12:50309800-50310200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:50310000-50310200	Enhancers	Esophagus	oesophagus
14	chr12:50310000-50310400	Enhancers	K562	blood

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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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