Variant report

Variant	rs6561555
Chromosome Location	chr13:50261977-50261978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50261388..50262971-chr13:50264534..50266295,2	K562	blood:
2	chr13:50261388..50263430-chr13:50264795..50266652,2	K562	blood:
3	chr13:50260531..50263061-chr13:50365546..50368292,2	K562	blood:
4	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
5	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:

Variant related genes	Relation type
ENSG00000123179	Chromatin interaction
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3809325	0.87[AFR][1000 genomes]
rs61959939	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561557	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319887	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7983918	0.81[AFR][1000 genomes]
rs9568306	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568307	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568312	0.90[ASN][1000 genomes]
rs9591292	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs6561555	EBPL	cis	Artery Tibial	GTEx
rs6561555	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 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	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
6	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
9	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
11	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
14	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
17	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
18	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
20	chr13:50251800-50262200	Weak transcription	Pancreas	Pancrea
21	chr13:50251800-50263600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:50253800-50264000	Weak transcription	Ovary	ovary
24	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:50254400-50264400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr13:50254400-50264400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:50254400-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:50254400-50264600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:50254400-50264600	Weak transcription	Esophagus	oesophagus
32	chr13:50254600-50264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:50255200-50264400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr13:50256000-50262000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:50256200-50264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:50256400-50263800	Weak transcription	NH-A	brain
37	chr13:50256400-50263800	Weak transcription	NHLF	lung
38	chr13:50256400-50264400	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:50256400-50264400	Weak transcription	Colonic Mucosa	Colon
40	chr13:50256400-50264400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr13:50256400-50264400	Weak transcription	NHDF-Ad	bronchial
42	chr13:50256600-50264200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:50256600-50264400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:50256600-50264400	Weak transcription	Brain Germinal Matrix	brain
45	chr13:50256600-50264600	Weak transcription	Placenta	Placenta
46	chr13:50256800-50263400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr13:50257000-50264000	Weak transcription	Fetal Brain Male	brain
48	chr13:50257200-50264400	Weak transcription	Fetal Brain Female	brain
49	chr13:50258200-50263200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:50258200-50264400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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