Variant report

Variant	rs55950921
Chromosome Location	chr15:50651463-50651464
allele	C/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	RAD21	chr15:50650819-50651522	SK-N-SH	brain:	n/a	chr15:50651219-50651228
2	RAD21	chr15:50651051-50651488	HepG2	liver:	n/a	chr15:50651219-50651228
3	RAD21	chr15:50650966-50651522	MCF-7	breast:	n/a	chr15:50651219-50651228
4	POLR2A	chr15:50651043-50651480	U87	brain:	n/a	n/a
5	RAD21	chr15:50651019-50651479	ECC-1	luminal epithelium:	n/a	chr15:50651219-50651228
6	CTCF	chr15:50650937-50651491	MCF-7	breast:	n/a	chr15:50651221-50651228
7	POLR2A	chr15:50650970-50651540	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:50650480-50651504	K562	blood:	n/a	n/a
9	SMC3	chr15:50650848-50651606	SK-N-SH	brain:	n/a	chr15:50651219-50651233
10	FOSL2	chr15:50650937-50651512	A549	lung:	n/a	chr15:50651238-50651246 chr15:50651235-50651243
11	RAD21	chr15:50651002-50651578	MCF-7	breast:	n/a	chr15:50651219-50651228
12	POLR2A	chr15:50651046-50651487	IMR90	lung:	n/a	n/a
13	CTCF	chr15:50651014-50651607	SK-N-SH	brain:	n/a	chr15:50651221-50651228
14	POLR2A	chr15:50643912-50651678	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr15:50650951-50651528	MCF-7	breast:	n/a	chr15:50651221-50651228
17	POLR2A	chr15:50650987-50651483	HepG2	liver:	n/a	n/a
18	POLR2A	chr15:50650962-50651526	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:50650822-50651524	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:50646088-50651672	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:50650925-50651495	HepG2	liver:	n/a	n/a
22	POLR2A	chr15:50651119-50651821	HepG2	liver:	n/a	n/a
23	POLR2A	chr15:50651118-50651496	PFSK-1	brain:	n/a	n/a
24	CTCF	chr15:50650759-50651585	A549	lung:	n/a	chr15:50651221-50651228

No.	Distal block	Cell Line	Cell type
1	chr15:50651100..50651692-chr15:50716599..50717183,2	MCF-7	breast:
2	chr15:50650545..50654228-chr15:50976566..50979826,3	MCF-7	breast:
3	chr1:119682098..119684548-chr15:50651200..50654157,2	MCF-7	breast:
4	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
5	chr15:50521669..50523479-chr15:50650112..50652205,2	MCF-7	breast:
6	chr15:50649363..50652046-chr15:51189573..51192655,3	MCF-7	breast:
7	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
8	chr15:50649633..50652207-chr15:51200859..51202821,2	K562	blood:
9	chr15:50547608..50550414-chr15:50649423..50651512,2	K562	blood:
10	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
11	chr15:50650650..50651693-chr15:51200046..51201235,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50650773-50651510	NONHSAT042412

Variant related genes	Relation type
GABPB1	TF binding region
MIR4712	TF binding region
ENSG00000231365	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000116874	Chromatin interaction
ENSG00000138592	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10083714	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10152574	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11491094	0.89[ASN][1000 genomes]
rs16963571	0.92[ASN][1000 genomes]
rs16963573	0.92[ASN][1000 genomes]
rs16963578	0.92[ASN][1000 genomes]
rs16963582	0.92[ASN][1000 genomes]
rs16963638	0.92[ASN][1000 genomes]
rs1896169	0.92[ASN][1000 genomes]
rs55697237	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55774471	0.92[ASN][1000 genomes]
rs55934154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56812974	0.92[ASN][1000 genomes]
rs58089987	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs58903525	0.92[ASN][1000 genomes]
rs59847008	0.92[ASN][1000 genomes]
rs60893904	0.92[ASN][1000 genomes]
rs717025	0.92[ASN][1000 genomes]
rs7177488	0.92[ASN][1000 genomes]
rs74012326	0.92[ASN][1000 genomes]
rs74012336	0.92[ASN][1000 genomes]
rs74012366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74012371	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs74012372	0.86[ASN][1000 genomes]
rs8028745	0.92[ASN][1000 genomes]
rs8029259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8029439	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8032042	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8032520	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8032602	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8032640	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8033413	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8033932	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8034492	0.92[ASN][1000 genomes]
rs8040420	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8040483	0.88[ASN][1000 genomes]
rs953159	0.92[ASN][1000 genomes]
rs9652452	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:50648200-50653800	Weak transcription	Pancreas	Pancrea
3	chr15:50648200-50657200	Weak transcription	Esophagus	oesophagus
4	chr15:50648200-50658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:50648200-50664400	Weak transcription	Lung	lung
6	chr15:50648400-50652800	Weak transcription	Ovary	ovary
7	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
8	chr15:50648800-50655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:50649000-50651600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:50649000-50653400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:50649000-50658600	Weak transcription	Right Atrium	heart
12	chr15:50649200-50652400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:50649200-50656400	Strong transcription	Fetal Muscle Leg	muscle
14	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
15	chr15:50649400-50651600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr15:50649400-50652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:50649400-50652400	Weak transcription	Brain Angular Gyrus	brain
18	chr15:50649400-50652600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr15:50649400-50653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:50649400-50653800	Weak transcription	Brain Anterior Caudate	brain
21	chr15:50649400-50653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:50649400-50653800	Weak transcription	Fetal Brain Female	brain
23	chr15:50649400-50653800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:50649400-50654800	Weak transcription	Brain Germinal Matrix	brain
25	chr15:50649400-50655800	Strong transcription	HSMM	muscle
26	chr15:50649400-50656600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:50649400-50657800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:50649400-50659200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:50649400-50664000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:50649600-50652200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:50649600-50652200	Weak transcription	HMEC	breast
32	chr15:50649600-50652400	Weak transcription	Adipose Nuclei	Adipose
33	chr15:50649600-50652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:50649600-50652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:50649600-50653000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr15:50649600-50654000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:50649600-50654600	Strong transcription	Osteobl	bone
38	chr15:50649600-50654800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:50649600-50654800	Weak transcription	Brain Substantia Nigra	brain
40	chr15:50649600-50655600	Weak transcription	Gastric	stomach
41	chr15:50649600-50656600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:50649600-50656800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:50649600-50657400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:50649600-50660600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:50649600-50661800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:50649800-50652200	Weak transcription	Liver	Liver
47	chr15:50649800-50652400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:50649800-50652800	Weak transcription	Fetal Stomach	stomach
49	chr15:50649800-50653600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:50649800-50653600	Strong transcription	Brain Hippocampus Middle	brain

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