Variant report

Variant	rs61959939
Chromosome Location	chr13:50264200-50264201
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50263387..50265868-chr13:50365424..50368677,3	K562	blood:
2	chr13:50219670..50221939-chr13:50262892..50264928,2	K562	blood:
3	chr13:50258208..50260676-chr13:50262902..50265227,2	K562	blood:
4	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
5	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:
6	chr13:50262508..50268089-chr13:50363531..50368771,13	MCF-7	breast:
7	chr13:50263387..50266299-chr13:50365424..50368132,3	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3809325	0.83[AFR][1000 genomes]
rs6561554	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561555	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561557	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7319887	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568306	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9568307	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568312	0.84[ASN][1000 genomes]
rs9591292	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61959939	EBPL	Cis_1M	lymphoblastoid	RTeQTL
rs61959939	EBPL	cis	Artery Tibial	GTEx

Chromatin state (count:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
2	chr13:50242200-50264200	Weak transcription	K562	blood
3	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
7	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
10	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
12	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
14	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:50254400-50264400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr13:50254400-50264400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:50254400-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:50254400-50264600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:50254400-50264600	Weak transcription	Esophagus	oesophagus
23	chr13:50254600-50264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:50255200-50264400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr13:50256200-50264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr13:50256400-50264400	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:50256400-50264400	Weak transcription	Colonic Mucosa	Colon
28	chr13:50256400-50264400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:50256400-50264400	Weak transcription	NHDF-Ad	bronchial
30	chr13:50256600-50264200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:50256600-50264400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:50256600-50264400	Weak transcription	Brain Germinal Matrix	brain
33	chr13:50256600-50264600	Weak transcription	Placenta	Placenta
34	chr13:50257200-50264400	Weak transcription	Fetal Brain Female	brain
35	chr13:50258200-50264400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr13:50259400-50264400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:50259800-50264400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr13:50260400-50264400	Weak transcription	Right Ventricle	heart
39	chr13:50260600-50264600	Weak transcription	Brain Anterior Caudate	brain
40	chr13:50261000-50264200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:50262200-50264400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr13:50262200-50264400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr13:50262200-50264400	Weak transcription	Fetal Thymus	thymus
44	chr13:50262200-50264800	Weak transcription	Gastric	stomach
45	chr13:50262400-50264200	Enhancers	Primary hematopoietic stem cells	blood
46	chr13:50262400-50264400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr13:50262400-50264600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr13:50262400-50264600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr13:50262400-50264800	Weak transcription	Spleen	Spleen
50	chr13:50262600-50264200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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