Variant report

Variant	rs16962687
Chromosome Location	chr15:49940997-49940998
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr15:49940890-49941125	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:49940952-49941152	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:49936634-49941675	K562	blood:	n/a	n/a
4	JUN	chr15:49940864-49941020	HepG2	liver:	n/a	chr15:49940981-49940994
5	POLR2A	chr15:49937746-49941045	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:49940965-49941102	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:49934468..49937629-chr15:49939008..49941773,3	K562	blood:
2	chr15:49935570..49938221-chr15:49938905..49941859,4	K562	blood:
3	chr15:49926539..49929038-chr15:49939808..49941780,2	K562	blood:
4	chr15:49911752..49916656-chr15:49939453..49943978,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261597	TF binding region
ENSG00000166262	Chromatin interaction
ENSG00000104047	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16962682	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs16962690	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16962694	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16962726	1.00[AMR][1000 genomes]
rs16962736	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs55820213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55880877	1.00[AMR][1000 genomes]
rs56194958	1.00[AMR][1000 genomes]
rs56365767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57224380	1.00[AMR][1000 genomes]
rs57402896	1.00[AMR][1000 genomes]
rs58984166	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59572993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59606072	1.00[AMR][1000 genomes]
rs60224127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60597223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61575085	1.00[AMR][1000 genomes]
rs61702984	1.00[AMR][1000 genomes]
rs7167875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7170176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012392	1.00[AMR][1000 genomes]
rs74012429	1.00[AMR][1000 genomes]
rs74012431	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012440	1.00[AMR][1000 genomes]
rs74012455	1.00[AFR][1000 genomes]
rs74012457	1.00[AMR][1000 genomes]
rs74012459	1.00[AMR][1000 genomes]
rs74012461	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74012490	1.00[AMR][1000 genomes]
rs74012491	1.00[AMR][1000 genomes]
rs74014148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74014149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74014150	1.00[AMR][1000 genomes]
rs74014340	1.00[AMR][1000 genomes]
rs74014341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74014352	1.00[AMR][1000 genomes]
rs8028992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033054	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8033587	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8035218	1.00[AFR][1000 genomes];1.00[AMR][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	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
2	chr15:49928200-49943000	Weak transcription	Lung	lung
3	chr15:49937000-49941000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:49937000-49941400	Weak transcription	Brain Germinal Matrix	brain
5	chr15:49937400-49942200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:49938200-49942200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:49938400-49942000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:49938400-49944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:49938400-49944600	Weak transcription	Ovary	ovary
10	chr15:49938400-49945400	Weak transcription	Fetal Heart	heart
11	chr15:49938600-49941000	Weak transcription	Fetal Kidney	kidney
12	chr15:49938800-49946200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:49939000-49941200	Weak transcription	Primary T cells from cord blood	blood
14	chr15:49939000-49941200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr15:49939000-49941400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:49939000-49943200	Weak transcription	Aorta	Aorta
17	chr15:49939000-49944400	Weak transcription	HSMMtube	muscle
18	chr15:49939000-49944600	Weak transcription	Osteobl	bone
19	chr15:49939000-49945000	Weak transcription	Left Ventricle	heart
20	chr15:49939200-49941400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:49939200-49941400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:49939200-49941600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:49939800-49942400	Weak transcription	NHDF-Ad	bronchial
24	chr15:49939800-49942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:49939800-49942800	Weak transcription	HSMM	muscle
26	chr15:49940000-49942000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:49940000-49944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:49940200-49941200	Enhancers	Hela-S3	cervix

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