Variant report

Variant	rs6561557
Chromosome Location	chr13:50265810-50265811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:311)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:311 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr13:50265688-50266026	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr13:50265323-50265962	GM10847	blood:	n/a	n/a
3	POLR2A	chr13:50265240-50265962	ECC-1	luminal epithelium:	n/a	n/a
4	MYBL2	chr13:50265391-50266000	HepG2	liver:	n/a	n/a
5	ELF1	chr13:50265078-50265880	GM12878	blood:	n/a	chr13:50265222-50265234
6	POLR2A	chr13:50265119-50265982	GM18505	blood:	n/a	n/a
7	POLR2A	chr13:50265248-50265885	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr13:50265502-50266142	HCT-116	colon:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
9	TCF12	chr13:50265651-50265923	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr13:50264807-50266122	MCF10A-Er-Src	breast:	n/a	chr13:50266048-50266058
11	POLR2A	chr13:50265348-50265963	GM18526	blood:	n/a	n/a
12	POLR2A	chr13:50265296-50265960	HUVEC	blood vessel:	n/a	n/a
13	MXI1	chr13:50265178-50265995	HepG2	liver:	n/a	n/a
14	E2F4	chr13:50265562-50266009	MCF10A-Er-Src	breast:	n/a	n/a
15	JUND	chr13:50265336-50266087	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUND	chr13:50265334-50265925	A549	lung:	n/a	n/a
17	POLR2A	chr13:50265300-50266015	PFSK-1	brain:	n/a	n/a
18	STAT1	chr13:50265326-50265984	GM12878	blood:	n/a	n/a
19	CEBPB	chr13:50265494-50266036	H1-hESC	embryonic stem cell:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
20	MYC	chr13:50265207-50265975	MCF-7	breast:	n/a	n/a
21	POLR2A	chr13:50265187-50266074	HUVEC	blood vessel:	n/a	n/a
22	CEBPB	chr13:50265712-50265917	HepG2	liver:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
23	TBL1XR1	chr13:50265672-50265892	GM12878	blood:	n/a	n/a
24	YY1	chr13:50265386-50265856	K562	blood:	n/a	n/a
25	MAX	chr13:50264970-50266242	A549	lung:	n/a	chr13:50266048-50266058
26	WRNIP1	chr13:50265809-50266017	GM12878	blood:	n/a	n/a
27	MAX	chr13:50265298-50266088	MCF-7	breast:	n/a	chr13:50266048-50266058
28	YY1	chr13:50265165-50265894	H1-hESC	embryonic stem cell:	n/a	chr13:50265229-50265238 chr13:50265224-50265238
29	POLR2A	chr13:50265232-50266035	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr13:50265559-50265935	K562	blood:	n/a	n/a
31	MYC	chr13:50265470-50265922	MCF-7	breast:	n/a	n/a
32	POLR2A	chr13:50265365-50265903	HepG2	liver:	n/a	n/a
33	POLR2A	chr13:50264839-50266021	GM12891	blood:	n/a	n/a
34	POLR2A	chr13:50264743-50266012	NB4	blood:	n/a	n/a
35	CEBPB	chr13:50265611-50266135	MCF-7	breast:	n/a	chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849 chr13:50265840-50265849
36	BCL3	chr13:50265588-50266085	A549	lung:	n/a	n/a
37	HEY1	chr13:50265365-50265907	K562	blood:	n/a	n/a
38	POLR2A	chr13:50265277-50265967	Hela-S3	cervix:	n/a	n/a
39	JUND	chr13:50265478-50265916	K562	blood:	n/a	n/a
40	POLR2A	chr13:50264906-50266121	H1-hESC	embryonic stem cell:	n/a	n/a
41	IRF1	chr13:50265502-50265811	K562	blood:	n/a	n/a
42	YY1	chr13:50264933-50266016	H1-hESC	embryonic stem cell:	n/a	chr13:50265229-50265238 chr13:50265224-50265238
43	POLR2A	chr13:50265426-50265969	K562	blood:	n/a	n/a
44	TAF1	chr13:50265100-50266018	ECC-1	luminal epithelium:	n/a	n/a
45	ZNF143	chr13:50265441-50265841	GM12878	blood:	n/a	n/a
46	MAFK	chr13:50265488-50265939	Hela-S3	cervix:	n/a	n/a
47	MAFF	chr13:50265610-50265896	HepG2	liver:	n/a	chr13:50265767-50265785
48	POLR2A	chr13:50265211-50266114	MCF-7	breast:	n/a	n/a
49	CTBP2	chr13:50265139-50265912	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr13:50265308-50265914	GM12891	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:50265802-50265852	PANC-1	pancreas:	n/a
2	chr13:50265802-50265852	BE2_C	brain:	n/a
3	chr13:50265802-50265852	NHBE	bronchial:	n/a
4	chr13:50265802-50265852	NB4	blood:	n/a
5	chr13:50265802-50265852	HAEpiC	amniotic membrane:	n/a
6	chr13:50265802-50265852	BJ	skin:	n/a
7	chr13:50265802-50265852	HMEC	breast:	n/a
8	chr13:50265802-50265852	Caco-2	colon:	n/a
9	chr13:50265802-50265852	HRE	kidney:	n/a
10	chr13:50265802-50265852	ECC-1	luminal epithelium:	n/a
11	chr13:50265802-50265852	AG04449	skin:	fetal
12	chr13:50265802-50265852	GM12892	blood:	n/a
13	chr13:50265802-50265852	K562	blood:	n/a
14	chr13:50265802-50265852	AoSMC	blood vessel:	n/a
15	chr13:50265802-50265852	AG09309	skin:	n/a
16	chr13:50265802-50265852	Hepatocyte	liver:	n/a
17	chr13:50265802-50265852	HEEpiC	esophagus:	n/a
18	chr13:50265802-50265852	NHDF-neo	bronchial:	n/a
19	chr13:50265802-50265852	HepG2	liver:	n/a
20	chr13:50265802-50265852	U87	brain:	n/a
21	chr13:50265802-50265852	NT2-D1	testis:	n/a
22	chr13:50265802-50265852	HNPCEpiC	eye:	n/a
23	chr13:50265802-50265852	SK-N-SH	brain:	n/a
24	chr13:50265802-50265852	HRPEpiC	eye:	n/a
25	chr13:50265802-50265852	SK-N-MC	brain:	n/a
26	chr13:50265802-50265852	T-47D	breast:	n/a
27	chr13:50265802-50265852	HCPEpiC	choroid plexus:	n/a
28	chr13:50265802-50265852	HCM	heart:	n/a
29	chr13:50265802-50265852	PFSK-1	brain:	n/a
30	chr13:50265802-50265852	HRCEpiC	kidney:	n/a
31	chr13:50265802-50265852	HEK293	kidney:	embryo
32	chr13:50265802-50265852	GM06990	blood:	n/a
33	chr13:50265802-50265852	AG10803	skin:	n/a
34	chr13:50265802-50265852	MCF10A-Er-Src	breast:	n/a
35	chr13:50265802-50265852	Jurkat	blood:	n/a
36	chr13:50265802-50265852	HL-60	blood:	n/a
37	chr13:50265802-50265852	HUVEC	blood vessel:	n/a
38	chr13:50265802-50265852	AG04450	lung:	fetal
39	chr13:50265802-50265852	PrEC	prostate:	n/a
40	chr13:50265802-50265852	GM12878	blood:	n/a
41	chr13:50265802-50265852	HPAEpiC	pulmonary alveolar:	n/a
42	chr13:50265802-50265852	NH-A	brain:	n/a
43	chr13:50265802-50265852	SK-N-SH_RA	brain:	n/a
44	chr13:50265802-50265852	H1-hESC	embryonic stem cell:	embryo
45	chr13:50265802-50265852	GM19239	blood:	n/a
46	chr13:50265802-50265852	GM12891	blood:	n/a
47	chr13:50265802-50265852	HIPEpiC	eye:	n/a
48	chr13:50265802-50265852	ovcar-3	ovarian:	n/a
49	chr13:50265802-50265852	A549	lung:	n/a
50	chr13:50265802-50265852	RPTEC	kidney:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50263387..50265868-chr13:50365424..50368677,3	K562	blood:
2	chr13:50265388..50266260-chr8:67837758..67838423,2	NB4	blood:
3	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
4	chr13:50265440..50265952-chr5:95997558..95998198,2	HCT-116	colon:
5	chr12:53701001..53701522-chr13:50265680..50266200,2	NB4	blood:
6	chr13:50265747..50268429-chr13:50268822..50272035,3	K562	blood:
7	chr13:50262508..50268089-chr13:50363531..50368771,13	MCF-7	breast:
8	chr13:50263387..50266299-chr13:50365424..50368132,3	K562	blood:

No data

Variant related genes	Relation type
EBPL	TF binding region
EBPL	CpG island
ENSG00000153113	Chromatin interaction
ENSG00000102753	Chromatin interaction
ENSG00000245910	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3809325	0.91[ASW][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs61959939	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561554	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561555	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319887	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7332209	0.84[CEU][hapmap]
rs7982132	0.84[ASW][hapmap];0.84[YRI][hapmap]
rs9526596	0.84[ASW][hapmap];0.84[YRI][hapmap]
rs9526599	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9535303	0.84[YRI][hapmap]
rs9535308	0.82[YRI][hapmap]
rs9535334	0.84[YRI][hapmap]
rs9535335	0.84[YRI][hapmap]
rs9562919	0.84[YRI][hapmap]
rs9568306	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568307	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568312	0.90[ASN][1000 genomes]
rs9568313	0.84[ASW][hapmap];0.84[YRI][hapmap]
rs9591292	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596183	0.82[ASW][hapmap];0.84[YRI][hapmap]
rs9596187	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6561557	ITM2B	cis	parietal	SCAN
rs6561557	EBPL	cis	Artery Tibial	GTEx
rs6561557	EBPL	cis	cerebellum	SCAN
rs6561557	EBPL	cis	multi-tissue	Pritchard
rs6561557	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50263600-50266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr13:50263800-50266200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:50264000-50266000	Active TSS	GM12878-XiMat	blood
4	chr13:50264000-50266200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:50264000-50266200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr13:50264000-50266200	Active TSS	HSMM	muscle
7	chr13:50264200-50266000	Active TSS	Lung	lung
8	chr13:50264200-50266000	Active TSS	Pancreas	Pancrea
9	chr13:50264200-50266200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr13:50264200-50266200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr13:50264200-50266200	Active TSS	Ovary	ovary
12	chr13:50264400-50266000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:50264400-50266000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr13:50264400-50266000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:50264400-50266000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr13:50264400-50266000	Active TSS	Fetal Intestine Large	intestine
17	chr13:50264400-50266000	Active TSS	A549	lung
18	chr13:50264400-50266200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr13:50264400-50266200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:50264400-50266200	Active TSS	Brain Cingulate Gyrus	brain
21	chr13:50264400-50266200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr13:50264400-50266200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:50264400-50266200	Active TSS	Fetal Intestine Small	intestine
24	chr13:50264400-50266200	Active TSS	Fetal Kidney	kidney
25	chr13:50264400-50266200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr13:50264400-50266200	Active TSS	Right Ventricle	heart
27	chr13:50264400-50266200	Active TSS	Thymus	Thymus
28	chr13:50264400-50266200	Active TSS	NHDF-Ad	bronchial
29	chr13:50264400-50266400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:50264400-50266400	Active TSS	Colonic Mucosa	Colon
31	chr13:50264400-50266400	Active TSS	Fetal Brain Female	brain
32	chr13:50264600-50266000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:50264600-50266000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:50264600-50266000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:50264600-50266000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:50264600-50266000	Active TSS	Right Atrium	heart
37	chr13:50264600-50266000	Active TSS	Stomach Smooth Muscle	stomach
38	chr13:50264600-50266200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:50264600-50266200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr13:50264600-50266200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr13:50264600-50266200	Active TSS	Brain Hippocampus Middle	brain
42	chr13:50264600-50266200	Active TSS	Left Ventricle	heart
43	chr13:50264600-50266200	Active TSS	Psoas Muscle	Psoas
44	chr13:50264600-50266200	Active TSS	Rectal Smooth Muscle	rectum
45	chr13:50264600-50266400	Active TSS	Esophagus	oesophagus
46	chr13:50264800-50266000	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr13:50264800-50266000	Active TSS	Brain Germinal Matrix	brain
48	chr13:50264800-50266000	Active TSS	Colon Smooth Muscle	Colon
49	chr13:50264800-50266000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr13:50264800-50266000	Active TSS	Small Intestine	intestine

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