Variant report

Variant	rs6561462
Chromosome Location	chr13:49153728-49153729
allele	A/G
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	HNF4G	chr13:49153692-49153948	HepG2	liver:	n/a	chr13:49153811-49153826 chr13:49153809-49153824
2	SPI1	chr13:49153164-49153876	HL-60	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
3	RUNX3	chr13:49152875-49153862	GM12878	blood:	n/a	n/a
4	RUNX3	chr13:49152656-49153923	GM12878	blood:	n/a	n/a
5	SPI1	chr13:49153173-49153839	GM12891	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
6	MAX	chr13:49153166-49154053	NB4	blood:	n/a	chr13:49153712-49153721 chr13:49153710-49153723
7	POLR2A	chr13:49152429-49154926	GM12891	blood:	n/a	n/a
8	NFIC	chr13:49152785-49153946	GM12878	blood:	n/a	n/a
9	BCLAF1	chr13:49153049-49153812	GM12878	blood:	n/a	chr13:49153493-49153502
10	TCF3	chr13:49153229-49153826	GM12878	blood:	n/a	n/a
11	MEF2A	chr13:49153153-49153837	GM12878	blood:	n/a	chr13:49153492-49153500
12	STAT3	chr13:49153324-49153815	MCF10A-Er-Src	breast:	n/a	chr13:49153580-49153591
13	MTA3	chr13:49152923-49153969	GM12878	blood:	n/a	n/a
14	YY1	chr13:49153642-49153943	GM12892	blood:	n/a	chr13:49153790-49153806 chr13:49153794-49153802
15	STAT5A	chr13:49152872-49153807	GM12878	blood:	n/a	chr13:49153580-49153591
16	MAX	chr13:49153283-49153945	GM12878	blood:	n/a	chr13:49153712-49153721 chr13:49153710-49153723
17	NFATC1	chr13:49153142-49153814	GM12878	blood:	n/a	n/a
18	RELA	chr13:49152601-49153982	GM15510	blood:	n/a	n/a
19	EP300	chr13:49153186-49153748	GM12878	blood:	n/a	chr13:49153488-49153502 chr13:49153586-49153595
20	YY1	chr13:49153347-49153957	GM12878	blood:	n/a	chr13:49153790-49153806 chr13:49153794-49153802
21	SPI1	chr13:49153263-49153836	GM12878	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
22	SPI1	chr13:49153205-49153772	GM12878	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
23	RAD21	chr13:49153604-49155108	SK-N-SH	brain:	n/a	chr13:49153823-49153837 chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
24	POU2F2	chr13:49153159-49153780	GM12878	blood:	n/a	n/a
25	EBF1	chr13:49152902-49153796	GM12878	blood:	n/a	n/a
26	STAT3	chr13:49153270-49153803	GM12878	blood:	n/a	chr13:49153580-49153591
27	RELA	chr13:49152698-49153985	GM12878	blood:	n/a	n/a
28	RCOR1	chr13:49153206-49153957	GM12878	blood:	n/a	n/a
29	BHLHE40	chr13:49153027-49153799	GM12878	blood:	n/a	n/a
30	ZNF384	chr13:49153264-49154849	GM12878	blood:	n/a	n/a
31	BCL11A	chr13:49153180-49153756	GM12878	blood:	n/a	chr13:49153493-49153502
32	MAZ	chr13:49152778-49153737	GM12878	blood:	n/a	chr13:49153712-49153721 chr13:49153710-49153723
33	STAT5A	chr13:49153251-49153774	GM12878	blood:	n/a	chr13:49153580-49153591
34	SPI1	chr13:49152845-49154231	GM12878	blood:	n/a	chr13:49153582-49153591 chr13:49153486-49153499 chr13:49153487-49153500 chr13:49153493-49153502 chr13:49153489-49153498
35	RAD21	chr13:49153216-49154041	GM12878	blood:	n/a	chr13:49153823-49153837
36	FOXM1	chr13:49152972-49153976	GM12878	blood:	n/a	n/a
37	TBL1XR1	chr13:49152801-49153879	GM12878	blood:	n/a	n/a
38	CUX1	chr13:49153266-49153835	GM12878	blood:	n/a	chr13:49153607-49153621
39	NFIC	chr13:49152700-49153982	GM12878	blood:	n/a	n/a
40	RELA	chr13:49152762-49153921	GM10847	blood:	n/a	n/a
41	IRF4	chr13:49153196-49153876	GM12878	blood:	n/a	n/a
42	YY1	chr13:49153612-49153892	GM12891	blood:	n/a	chr13:49153790-49153806 chr13:49153794-49153802
43	EP300	chr13:49153045-49153782	GM12878	blood:	n/a	chr13:49153488-49153502 chr13:49153586-49153595
44	ELK1	chr13:49153300-49153780	GM12878	blood:	n/a	n/a
45	MEF2A	chr13:49152915-49153770	GM12878	blood:	n/a	chr13:49153492-49153500
46	ATF2	chr13:49153159-49153854	GM12878	blood:	n/a	n/a
47	WRNIP1	chr13:49152761-49154036	GM12878	blood:	n/a	n/a
48	MXI1	chr13:49153318-49153842	GM12878	blood:	n/a	n/a
49	YY1	chr13:49153275-49153969	GM12878	blood:	n/a	chr13:49153790-49153806 chr13:49153794-49153802
50	POLR2A	chr13:49153108-49153755	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48806307..48808548-chr13:49152200..49154470,2	MCF-7	breast:
2	chr13:48908843..48909363-chr13:49153698..49154640,2	MCF-7	breast:

Variant related genes	Relation type
LINC00462	TF binding region
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4151636	1.00[ASN][1000 genomes]
rs6420296	1.00[ASN][1000 genomes]
rs6561464	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997110	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6561462	MED4	cis	parietal	SCAN
rs6561462	CPB2	cis	parietal	SCAN
rs6561462	C13orf18	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49146000-49153800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr13:49146400-49154000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:49146800-49157400	Weak transcription	HSMMtube	muscle
5	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
6	chr13:49148400-49153800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr13:49148400-49153800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
10	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr13:49148600-49153800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:49148800-49153800	Weak transcription	Brain Substantia Nigra	brain
13	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:49150400-49154200	Enhancers	Fetal Thymus	thymus
15	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr13:49152400-49154000	Enhancers	Spleen	Spleen
17	chr13:49152400-49154200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr13:49152400-49155000	Enhancers	Dnd41	blood
19	chr13:49152600-49154000	Enhancers	Esophagus	oesophagus
20	chr13:49152600-49154800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:49152600-49155000	Enhancers	Brain Anterior Caudate	brain
22	chr13:49152600-49155400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:49152800-49154000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:49152800-49154000	Enhancers	Fetal Muscle Leg	muscle
25	chr13:49152800-49154000	Enhancers	Placenta	Placenta
26	chr13:49152800-49154200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:49152800-49154400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr13:49152800-49154400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:49152800-49155000	Enhancers	HepG2	liver
31	chr13:49152800-49155200	Enhancers	Brain Hippocampus Middle	brain
32	chr13:49152800-49155400	Enhancers	HMEC	breast
33	chr13:49153000-49154000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr13:49153000-49154200	Enhancers	Adipose Nuclei	Adipose
35	chr13:49153000-49154200	Enhancers	Duodenum Mucosa	Duodenum
36	chr13:49153000-49154200	Enhancers	Fetal Intestine Small	intestine
37	chr13:49153000-49154800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr13:49153200-49154000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr13:49153200-49154000	Enhancers	Small Intestine	intestine
40	chr13:49153200-49154400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:49153200-49154600	Enhancers	Primary B cells from peripheral blood	blood
42	chr13:49153200-49154800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr13:49153200-49154800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr13:49153200-49155000	Enhancers	Stomach Mucosa	stomach
45	chr13:49153200-49155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:49153400-49153800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:49153400-49153800	Weak transcription	Right Atrium	heart
48	chr13:49153400-49154600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr13:49153400-49154800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr13:49153400-49155000	Enhancers	Brain Cingulate Gyrus	brain

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