Variant report

Variant	rs4549456
Chromosome Location	chr4:56264753-56264754
allele	C/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	FOXA1	chr4:56264652-56264957	HepG2	liver:	n/a	n/a
2	FOXA1	chr4:56264642-56264986	HepG2	liver:	n/a	n/a
3	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
4	BHLHE40	chr4:56264739-56264818	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:56264595-56264980	U87	brain:	n/a	n/a
6	FOS	chr4:56264209-56265894	MCF10A-Er-Src	breast:	n/a	n/a
7	JUND	chr4:56264366-56265013	K562	blood:	n/a	n/a
8	MYC	chr4:56264187-56265000	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr4:56264021-56264832	Hela-S3	cervix:	n/a	chr4:56264724-56264733 chr4:56264721-56264735 chr4:56264720-56264736 chr4:56264720-56264736
10	WRNIP1	chr4:56264024-56264889	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:56264053-56264904	HepG2	liver:	n/a	n/a
12	CEBPB	chr4:56264165-56265001	IMR90	lung:	n/a	chr4:56264368-56264379
13	FOXA2	chr4:56264664-56264947	HepG2	liver:	n/a	n/a
14	STAT3	chr4:56263026-56265466	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56263633-56263641 chr4:56264742-56264753
15	POLR2A	chr4:56264702-56264974	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr4:56263981-56264888	GM12878	blood:	n/a	n/a
17	ARID3A	chr4:56264297-56265424	HepG2	liver:	n/a	n/a
18	TBL1XR1	chr4:56264158-56264927	K562	blood:	n/a	n/a
19	POLR2A	chr4:56264557-56264893	K562	blood:	n/a	n/a
20	TCF7L2	chr4:56264187-56264864	HEK293	kidney:	n/a	chr4:56264724-56264733 chr4:56264721-56264735 chr4:56264720-56264736 chr4:56264720-56264736
21	GATA1	chr4:56264211-56265348	PBDE	blood:	n/a	chr4:56264840-56264849
22	POLR2A	chr4:56263945-56265097	U87	brain:	n/a	n/a
23	POLR2A	chr4:56261304-56265017	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr4:56263800-56264762	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr4:56261116-56266115	IMR90	lung:	n/a	n/a
26	MXI1	chr4:56261402-56265198	IMR90	lung:	n/a	n/a
27	TCF7L2	chr4:56264599-56265090	PANC-1	pancreas:	n/a	chr4:56264724-56264733 chr4:56264721-56264735 chr4:56264720-56264736 chr4:56264720-56264736
28	KAP1	chr4:56263744-56264951	HEK293	kidney:	n/a	chr4:56264742-56264750
29	POLR2A	chr4:56264032-56264770	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr4:56263918-56265146	U87	brain:	n/a	n/a
31	CUX1	chr4:56264372-56265037	K562	blood:	n/a	n/a
32	FOS	chr4:56264180-56265531	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr4:56264307-56264849	K562	blood:	n/a	chr4:56264744-56264758
34	POLR2A	chr4:56261470-56264938	GM12878	blood:	n/a	n/a
35	CHD1	chr4:56261060-56266047	IMR90	lung:	n/a	n/a
36	POLR2A	chr4:56264045-56265557	PBDE	blood:	n/a	n/a
37	MYC	chr4:56264221-56265284	MCF10A-Er-Src	breast:	n/a	n/a
38	FOXA1	chr4:56264681-56264904	T-47D	breast:	n/a	n/a
39	FOXA1	chr4:56264614-56264949	HepG2	liver:	n/a	n/a
40	STAT3	chr4:56264173-56265531	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
41	ZNF384	chr4:56263693-56265212	K562	blood:	n/a	n/a
42	MAX	chr4:56264702-56264978	K562	blood:	n/a	n/a
43	STAT3	chr4:56264128-56265365	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
44	POLR2A	chr4:56264249-56265911	K562	blood:	n/a	n/a
45	BHLHE40	chr4:56264584-56264914	K562	blood:	n/a	n/a
46	STAT3	chr4:56264123-56265002	Hela-S3	cervix:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
47	POLR2A	chr4:56264723-56264977	K562	blood:	n/a	n/a
48	FOS	chr4:56264233-56265510	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr4:56264209-56264766	A549	lung:	n/a	n/a
50	TEAD4	chr4:56263787-56265060	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
3	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
4	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
5	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
6	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
7	chr4:56247536..56249762-chr4:56263632..56266279,3	K562	blood:
8	chr4:56216631..56219343-chr4:56262936..56265336,2	K562	blood:
9	chr17:46126036..46126788-chr4:56264311..56264974,2	Hela-S3	cervix:
10	chr4:56262170..56264152-chr4:56264363..56265916,3	K562	blood:
11	chr4:56216631..56219493-chr4:56263836..56266245,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRD5A3-4	chr4:56264559-56265055	NONHSAT096458

Variant related genes	Relation type
TMEM165	TF binding region
SRD5A3-AS1	TF binding region
ENSG00000251111	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10049561	0.84[ASN][1000 genomes]
rs11732723	0.86[ASN][1000 genomes]
rs11943456	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13113860	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3749472	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3749473	0.86[ASN][1000 genomes]
rs6810483	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6828454	0.86[ASN][1000 genomes]
rs6840236	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6858749	0.86[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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4549456	TMEM165	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56261200-56264800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56261200-56265200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:56261400-56264800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:56261400-56264800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:56261400-56264800	Active TSS	Fetal Kidney	kidney
6	chr4:56261400-56264800	Active TSS	Ovary	ovary
7	chr4:56261400-56264800	Active TSS	Right Ventricle	heart
8	chr4:56261400-56265000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr4:56261400-56265200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:56261400-56265200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:56261400-56265200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr4:56261400-56265400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:56261400-56265400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:56261400-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:56261400-56265400	Active TSS	Aorta	Aorta
16	chr4:56261400-56265400	Active TSS	Lung	lung
17	chr4:56261400-56265400	Active TSS	Psoas Muscle	Psoas
18	chr4:56261400-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr4:56261400-56265600	Active TSS	HSMMtube	muscle
20	chr4:56261400-56266000	Active TSS	Right Atrium	heart
21	chr4:56261600-56264800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:56261600-56265200	Active TSS	NHDF-Ad	bronchial
23	chr4:56261600-56265200	Active TSS	NHLF	lung
24	chr4:56261600-56265400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr4:56261600-56265400	Active TSS	Pancreas	Pancrea
26	chr4:56261600-56265400	Active TSS	GM12878-XiMat	blood
27	chr4:56261600-56266000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:56262400-56265000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr4:56262400-56265600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:56262600-56265200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:56262600-56265400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:56262800-56265000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr4:56262800-56265000	Flanking Active TSS	Fetal Brain Male	brain
34	chr4:56262800-56265400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:56262800-56265600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr4:56262800-56266000	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr4:56263000-56264800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:56263200-56264800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr4:56263200-56265200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr4:56263400-56265000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr4:56263400-56265800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
42	chr4:56263400-56265800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr4:56263400-56265800	Transcr. at gene 5' and 3'	NHEK	skin
44	chr4:56263400-56265800	Transcr. at gene 5' and 3'	Osteobl	bone
45	chr4:56263400-56266000	Transcr. at gene 5' and 3'	K562	blood
46	chr4:56263600-56264800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr4:56263600-56265600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:56263600-56265800	Enhancers	Fetal Heart	heart
49	chr4:56263600-56266000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:56263600-56266000	Enhancers	Primary B cells from peripheral blood	blood

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