Variant report

Variant	rs2899620
Chromosome Location	chr15:58525399-58525400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58516526..58518271-chr15:58524056..58526534,2	K562	blood:
2	chr15:58524274..58525988-chr15:58623095..58624851,2	K562	blood:

Variant related genes	Relation type
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11631950	0.80[TSI][hapmap]
rs11855432	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1320053	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1663251	0.81[EUR][1000 genomes]
rs1663252	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1663257	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16939937	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs1711033	0.90[ASN][1000 genomes]
rs2414558	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs55803039	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55825503	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56168508	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57753445	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62000511	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62000517	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493989	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175693	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7175710	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7182088	0.91[ASN][1000 genomes]
rs8034444	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8034953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv833024	chr15:58447459-58621963	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1050473	chr15:58479888-58562270	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv904264	chr15:58505122-58588510	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv904265	chr15:58517528-58588510	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
7	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58521400-58525400	Weak transcription	Hela-S3	cervix
2	chr15:58521400-58534200	Weak transcription	Liver	Liver
3	chr15:58522000-58525600	Weak transcription	A549	lung
4	chr15:58522400-58526200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:58522400-58528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:58522600-58526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:58522600-58526200	Weak transcription	HSMMtube	muscle
8	chr15:58522800-58526000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:58522800-58532200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:58523200-58528200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:58523200-58531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:58523200-58537800	Weak transcription	Left Ventricle	heart
13	chr15:58523600-58526600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:58523800-58525600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:58524000-58526400	Enhancers	HMEC	breast
16	chr15:58524200-58525400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:58524200-58528800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:58524400-58526600	Flanking Active TSS	NHEK	skin
19	chr15:58524400-58528800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:58524600-58526000	Weak transcription	Placenta	Placenta
21	chr15:58524800-58525400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr15:58524800-58547400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:58525000-58531800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:58525000-58535200	Weak transcription	Right Atrium	heart

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