Variant report

Variant	rs57496745
Chromosome Location	chr15:49939572-49939573
allele	G/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
3	POLR2A	chr15:49937277-49939793	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	chr15:49934440..49937340-chr15:49937772..49940035,3	MCF-7	breast:
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: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12591533	0.82[ASN][1000 genomes]
rs12594585	0.86[ASN][1000 genomes]
rs12595447	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17482833	0.90[ASN][1000 genomes]
rs34833569	0.82[ASN][1000 genomes]
rs58275754	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59589271	0.85[ASN][1000 genomes]
rs72729121	0.82[ASN][1000 genomes]
rs72729125	0.84[ASN][1000 genomes]
rs72729127	0.85[ASN][1000 genomes]
rs72729130	0.84[ASN][1000 genomes]
rs72729132	0.85[ASN][1000 genomes]
rs72729199	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72731108	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72731111	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72731116	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72731119	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72731121	0.84[EUR][1000 genomes]
rs72731122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72731125	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731137	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72731140	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72731160	0.80[AMR][1000 genomes];0.83[ASN][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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
2	chr15:49919800-49940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:49920000-49940400	Weak transcription	A549	lung
4	chr15:49920800-49940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:49927000-49940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:49928000-49940200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:49928200-49939600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:49928200-49940400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:49928200-49940600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:49928200-49943000	Weak transcription	Lung	lung
11	chr15:49928400-49939800	Weak transcription	HUVEC	blood vessel
12	chr15:49936000-49939800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:49936600-49940400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:49936800-49940600	Weak transcription	Fetal Thymus	thymus
15	chr15:49937000-49939600	Weak transcription	K562	blood
16	chr15:49937000-49939800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:49937000-49939800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:49937000-49940000	Weak transcription	Small Intestine	intestine
19	chr15:49937000-49941000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:49937000-49941400	Weak transcription	Brain Germinal Matrix	brain
21	chr15:49937200-49939600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:49937200-49940200	Weak transcription	Dnd41	blood
23	chr15:49937400-49940400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:49937400-49940600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr15:49937400-49942200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:49938200-49939800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:49938200-49942200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:49938400-49939800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:49938400-49939800	Strong transcription	HSMM	muscle
30	chr15:49938400-49940800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:49938400-49942000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:49938400-49944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:49938400-49944600	Weak transcription	Ovary	ovary
34	chr15:49938400-49945400	Weak transcription	Fetal Heart	heart
35	chr15:49938600-49940600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:49938600-49940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:49938600-49941000	Weak transcription	Fetal Kidney	kidney
38	chr15:49938800-49940000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:49938800-49940200	Weak transcription	Right Atrium	heart
40	chr15:49938800-49940400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:49938800-49946200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:49939000-49940000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:49939000-49940000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:49939000-49940400	Weak transcription	NHLF	lung
45	chr15:49939000-49941200	Weak transcription	Primary T cells from cord blood	blood
46	chr15:49939000-49941200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:49939000-49941400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:49939000-49943200	Weak transcription	Aorta	Aorta
49	chr15:49939000-49944400	Weak transcription	HSMMtube	muscle
50	chr15:49939000-49944600	Weak transcription	Osteobl	bone

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