Variant report

Variant	rs62020397
Chromosome Location	chr15:50169495-50169496
allele	A/C
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	RAD21	chr15:50168826-50169511	HCT-116	colon:	n/a	chr15:50169138-50169157
2	CTCF	chr15:50168965-50169707	GM12878	blood:	n/a	chr15:50169139-50169160 chr15:50169137-50169155
3	CTCF	chr15:50169476-50169519	Pancreas_OC	pancreas:	n/a	n/a
4	CHD2	chr15:50168946-50169592	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr15:50169490-50169648	GM12878	blood:	n/a	n/a
6	CTCF	chr15:50169460-50169610	HCFaa	heart:	n/a	n/a
7	CTCF	chr15:50169440-50169590	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr15:50168956-50169717	K562	blood:	n/a	chr15:50169139-50169160 chr15:50169137-50169155
9	RAD21	chr15:50168873-50169751	MCF-7	breast:	n/a	chr15:50169138-50169157
10	RAD21	chr15:50168964-50169635	Hela-S3	cervix:	n/a	chr15:50169138-50169157
11	CTCF	chr15:50169460-50169610	HVMF	connective:	n/a	n/a
12	CTCF	chr15:50169363-50169714	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZNF143	chr15:50168939-50169506	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr15:50169438-50169637	GM12878	blood:	n/a	n/a
15	CTCF	chr15:50168760-50169765	MCF-7	breast:	n/a	chr15:50169139-50169160 chr15:50169137-50169155
16	CTCF	chr15:50169480-50169630	AG09319	gingival:	n/a	n/a
17	MAZ	chr15:50169436-50169526	Hela-S3	cervix:	n/a	n/a
18	SIN3A	chr15:50168965-50169602	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr15:50168908-50169903	H1-hESC	embryonic stem cell:	n/a	chr15:50169138-50169157
20	CTCF	chr15:50169460-50169610	HMEC	breast:	n/a	n/a
21	CTCF	chr15:50169460-50169610	K562	blood:	n/a	n/a
22	CTCF	chr15:50169460-50169610	NHDF-neo	bronchial:	n/a	n/a
23	SMC3	chr15:50168989-50169568	GM12878	blood:	n/a	n/a
24	CTCF	chr15:50169460-50169610	AG10803	skin:	n/a	n/a
25	CTCF	chr15:50169351-50169717	H1-hESC	embryonic stem cell:	n/a	n/a
26	SMC3	chr15:50168952-50169588	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr15:50169380-50169530	MCF-7	breast:	n/a	n/a
28	RAD21	chr15:50168939-50169747	H1-hESC	embryonic stem cell:	n/a	chr15:50169138-50169157
29	RAD21	chr15:50168840-50169844	H1-hESC	embryonic stem cell:	n/a	chr15:50169138-50169157
30	CTCF	chr15:50169480-50169630	HMF	breast:	n/a	n/a
31	CTCF	chr15:50169480-50169630	NHDF-neo	bronchial:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:186344519..186345079-chr15:50169033..50169608,2	MCF-7	breast:
2	chr15:50168979..50170922-chr15:50428589..50430451,2	MCF-7	breast:
3	chr15:50169219..50170062-chrX:139654632..139655476,2	MCF-7	breast:
4	chr15:49911713..49913388-chr15:50169231..50171069,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGF7-1	chr15:50169490-50169625	NONHSAT042394
2	lnc-FGF7-1	chr15:50169490-50169625	NONHSAT042392
3	lnc-FGF7-1	chr15:50169490-50169625	NONHSAT042395
4	lnc-FGF7-1	chr15:50169490-50169625	NONHSAT042393

Variant related genes	Relation type
ENSG00000259188	TF binding region
ATP8B4	TF binding region
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction
ENSG00000157181	Chromatin interaction
ENSG00000047410	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12441351	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17487348	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7342629	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	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
2	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
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50135800-50187400	Weak transcription	Liver	Liver
3	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50158800-50170600	Weak transcription	Placenta	Placenta
7	chr15:50161600-50175600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:50161800-50179000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:50162400-50172200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:50163000-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:50166000-50170800	Weak transcription	Left Ventricle	heart
13	chr15:50166600-50170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:50166600-50173000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:50167000-50171600	Enhancers	Colon Smooth Muscle	Colon
16	chr15:50167200-50171200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:50167600-50200800	Weak transcription	Spleen	Spleen
18	chr15:50168200-50171800	Enhancers	Rectal Smooth Muscle	rectum
19	chr15:50168400-50169600	Enhancers	Pancreas	Pancrea
20	chr15:50168400-50169600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr15:50168400-50169600	Enhancers	Small Intestine	intestine
22	chr15:50168400-50169800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:50168400-50170000	Enhancers	Aorta	Aorta
24	chr15:50168400-50170200	Enhancers	Fetal Lung	lung
25	chr15:50168400-50170200	Enhancers	Ovary	ovary
26	chr15:50168400-50170800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:50168400-50171200	Enhancers	Fetal Muscle Leg	muscle
28	chr15:50168400-50171400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:50168400-50171400	Enhancers	NHDF-Ad	bronchial
30	chr15:50168400-50172600	Enhancers	Fetal Stomach	stomach
31	chr15:50168600-50169600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:50168600-50169800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr15:50168600-50169800	Enhancers	Hela-S3	cervix
34	chr15:50168600-50171200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:50168600-50171200	Enhancers	Fetal Kidney	kidney
36	chr15:50168600-50171200	Enhancers	Right Atrium	heart
37	chr15:50168600-50171200	Enhancers	Osteobl	bone
38	chr15:50168800-50169800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr15:50168800-50170600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr15:50168800-50171000	Enhancers	Adipose Nuclei	Adipose
41	chr15:50169000-50169600	Enhancers	Brain Hippocampus Middle	brain
42	chr15:50169200-50169600	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:50169200-50169600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:50169200-50169800	Enhancers	Brain Substantia Nigra	brain
45	chr15:50169200-50169800	Enhancers	Stomach Mucosa	stomach
46	chr15:50169200-50170000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr15:50169200-50171200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:50169200-50171200	Enhancers	NHLF	lung
49	chr15:50169400-50169600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:50169400-50169600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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