Variant report

Variant	rs1549960
Chromosome Location	chr19:42262600-42262601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11669653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459454	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1805223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3795018	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3795020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803507	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57827663	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3384883	chr19:42253458-42288853	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3319044	chr19:42257039-42297123	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3319045	chr19:42257039-42297123	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2763205	chr19:42258547-42290598	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv911775	chr19:42259228-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42257600-42262600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:42259200-42263000	Active TSS	Esophagus	oesophagus
3	chr19:42259400-42262800	Active TSS	Colonic Mucosa	Colon
4	chr19:42259600-42262600	Active TSS	Lung	lung
5	chr19:42260400-42262800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr19:42260800-42262600	Enhancers	Fetal Intestine Small	intestine
7	chr19:42261000-42262600	Enhancers	Duodenum Mucosa	Duodenum
8	chr19:42261000-42263000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr19:42261800-42263200	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:42262000-42266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr19:42262400-42262600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:42262400-42262600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:42262400-42262800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:42262400-42263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:42262600-42262800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr19:42262600-42263000	Flanking Active TSS	Lung	lung
17	chr19:42262600-42263400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:42262600-42263600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:42262600-42270400	Weak transcription	Fetal Intestine Small	intestine

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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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