Variant report

Variant	rs9920705
Chromosome Location	chr15:49940757-49940758
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	POLR2A	chr15:49936634-49941675	K562	blood:	n/a	n/a
2	POLR2A	chr15:49937746-49941045	Hela-S3	cervix:	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: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10519233	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13329455	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1354918	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1588127	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17402569	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17404262	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17480434	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17481696	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17482833	0.91[AFR][1000 genomes]
rs17483139	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28393768	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28408092	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28409376	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28430272	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28465200	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28484276	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28492008	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28516445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28568399	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28635979	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28669217	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28671247	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28798135	0.84[AMR][1000 genomes]
rs28843724	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3210227	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8040716	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9920574	0.92[AMR][1000 genomes];0.87[EUR][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:31 , 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	chr15:49938400-49940800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:49938400-49942000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:49938400-49944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:49938400-49944600	Weak transcription	Ovary	ovary
11	chr15:49938400-49945400	Weak transcription	Fetal Heart	heart
12	chr15:49938600-49940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:49938600-49941000	Weak transcription	Fetal Kidney	kidney
14	chr15:49938800-49946200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:49939000-49941200	Weak transcription	Primary T cells from cord blood	blood
16	chr15:49939000-49941200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:49939000-49941400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:49939000-49943200	Weak transcription	Aorta	Aorta
19	chr15:49939000-49944400	Weak transcription	HSMMtube	muscle
20	chr15:49939000-49944600	Weak transcription	Osteobl	bone
21	chr15:49939000-49945000	Weak transcription	Left Ventricle	heart
22	chr15:49939200-49941400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:49939200-49941400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:49939200-49941600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:49939800-49942400	Weak transcription	NHDF-Ad	bronchial
26	chr15:49939800-49942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:49939800-49942800	Weak transcription	HSMM	muscle
28	chr15:49940000-49942000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:49940000-49944400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:49940200-49941200	Enhancers	Hela-S3	cervix
31	chr15:49940600-49940800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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