Variant report

Variant	rs554335631
Chromosome Location	chr1:154159592-154159593
allele	G/T
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	JUN	chr1:154159505-154159934	K562	blood:	n/a	n/a
2	MYC	chr1:154159419-154159906	K562	blood:	n/a	n/a
3	CBX3	chr1:154159565-154159900	K562	blood:	n/a	n/a
4	ZNF384	chr1:154159311-154159905	K562	blood:	n/a	n/a
5	POLR2A	chr1:154159549-154159826	K562	blood:	n/a	n/a
6	TBL1XR1	chr1:154159374-154159827	K562	blood:	n/a	n/a
7	CBX3	chr1:154159525-154159938	K562	blood:	n/a	n/a
8	MAFK	chr1:154159334-154159924	K562	blood:	n/a	n/a
9	TRIM28	chr1:154159232-154160029	K562	blood:	n/a	n/a
10	ZMIZ1	chr1:154159248-154159864	K562	blood:	n/a	n/a
11	CEBPD	chr1:154158708-154159966	K562	blood:	n/a	n/a
12	POLR2A	chr1:154159443-154160121	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAFK	chr1:154159380-154159912	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr1:154159142-154159987	K562	blood:	n/a	n/a
15	TAL1	chr1:154159192-154159925	K562	blood:	n/a	n/a
16	CEBPB	chr1:154158897-154160345	K562	blood:	n/a	chr1:154159149-154159160
17	MAFF	chr1:154159591-154159927	K562	blood:	n/a	chr1:154159793-154159811
18	ARID3A	chr1:154158624-154159915	K562	blood:	n/a	n/a
19	ZBTB7A	chr1:154159527-154159749	K562	blood:	n/a	n/a
20	MAX	chr1:154159539-154159826	K562	blood:	n/a	n/a
21	KAP1	chr1:154158534-154159988	U2OS	brain:	n/a	n/a
22	FOXA1	chr1:154158986-154159857	HepG2	liver:	n/a	chr1:154159380-154159395 chr1:154159450-154159462
23	MAZ	chr1:154159424-154159902	K562	blood:	n/a	n/a
24	CEBPD	chr1:154159286-154160016	K562	blood:	n/a	n/a
25	FOXA1	chr1:154159013-154159637	T-47D	breast:	n/a	chr1:154159380-154159395 chr1:154159450-154159462
26	HCFC1	chr1:154159512-154159872	K562	blood:	n/a	n/a
27	EP300	chr1:154158622-154159934	K562	blood:	n/a	chr1:154159453-154159463
28	GATA3	chr1:154158545-154159715	MCF-7	breast:	n/a	chr1:154159690-154159697 chr1:154158800-154158808 chr1:154158892-154158901 chr1:154159690-154159697 chr1:154158550-154158571 chr1:154159688-154159698 chr1:154159690-154159697
29	RUNX3	chr1:154159568-154159964	GM12878	blood:	n/a	n/a
30	RCOR1	chr1:154158609-154159949	K562	blood:	n/a	n/a
31	RCOR1	chr1:154159365-154159825	K562	blood:	n/a	n/a
32	GATA2	chr1:154159140-154159942	K562	blood:	n/a	chr1:154159690-154159697 chr1:154159690-154159697 chr1:154159688-154159698 chr1:154159690-154159697
33	CCNT2	chr1:154159243-154159880	K562	blood:	n/a	n/a
34	ESR1	chr1:154159182-154159843	T-47D	breast:	n/a	n/a
35	FOXA2	chr1:154159562-154159908	HepG2	liver:	n/a	n/a
36	JUND	chr1:154159349-154159920	K562	blood:	n/a	chr1:154159495-154159504
37	FOXA1	chr1:154159091-154159982	HepG2	liver:	n/a	chr1:154159380-154159395 chr1:154159450-154159462
38	EP300	chr1:154159442-154159845	K562	blood:	n/a	chr1:154159453-154159463
39	TEAD4	chr1:154159230-154159948	K562	blood:	n/a	n/a
40	TBL1XR1	chr1:154159213-154159935	K562	blood:	n/a	n/a
41	CUX1	chr1:154159270-154159859	K562	blood:	n/a	n/a
42	NR2F2	chr1:154159208-154159914	K562	blood:	n/a	n/a
43	MAX	chr1:154159469-154159863	K562	blood:	n/a	n/a
44	CEBPB	chr1:154159577-154159982	ECC-1	luminal epithelium:	n/a	n/a
45	STAT5A	chr1:154159516-154159890	K562	blood:	n/a	n/a
46	STAT5A	chr1:154159277-154159906	K562	blood:	n/a	n/a
47	NR2F2	chr1:154159159-154160018	K562	blood:	n/a	n/a
48	ATF1	chr1:154159321-154159871	K562	blood:	n/a	n/a
49	CEBPB	chr1:154158935-154159958	K562	blood:	n/a	chr1:154159149-154159160
50	KAP1	chr1:154158572-154159942	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154159154..154160815-chr1:154163047..154164875,2	MCF-7	breast:
2	chr1:154158539..154161524-chr1:154242189..154245561,3	MCF-7	breast:
3	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
4	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
5	chr1:154158467..154161316-chr1:154169815..154172829,3	MCF-7	breast:
6	chr1:154129855..154131682-chr1:154158722..154160655,2	K562	blood:
7	chr1:153963252..153965177-chr1:154158511..154161067,3	MCF-7	breast:
8	chr1:154158424..154161181-chr1:154245114..154247197,2	MCF-7	breast:
9	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
10	chr1:154157441..154159782-chr1:154297521..154299444,2	MCF-7	breast:
11	chr1:154159143..154160750-chr1:154457957..154460845,2	MCF-7	breast:
12	chr1:154158378..154160175-chr1:154161458..154162989,2	K562	blood:
13	chr1:154158089..154161877-chr1:154191453..154195317,5	K562	blood:
14	chr1:154155278..154160143-chr1:154165338..154167782,4	K562	blood:
15	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
16	chr1:154157620..154160474-chr1:154243122..154244827,3	MCF-7	breast:

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000215938	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000169291	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000143569	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3453084	chr1:154156328-154161626	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3453085	chr1:154156328-154161626	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv12863	chr1:154158242-154161302	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154156200-154163000	Weak transcription	Psoas Muscle	Psoas
2	chr1:154156400-154159600	Weak transcription	GM12878-XiMat	blood
3	chr1:154156400-154163200	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:154156400-154164200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:154156600-154164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:154156800-154164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:154157200-154164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:154158000-154159600	Enhancers	Hela-S3	cervix
9	chr1:154158200-154159600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:154158200-154159800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:154158400-154159600	Enhancers	HSMM	muscle
12	chr1:154158400-154159800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:154158400-154159800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:154158400-154159800	Enhancers	Fetal Intestine Small	intestine
15	chr1:154158400-154160200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr1:154158400-154160200	Enhancers	HepG2	liver
17	chr1:154158400-154160400	Enhancers	Stomach Mucosa	stomach
18	chr1:154158400-154160600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:154158600-154160600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:154158800-154159600	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:154158800-154159800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:154158800-154159800	Enhancers	Fetal Intestine Large	intestine
23	chr1:154158800-154160000	Flanking Active TSS	K562	blood
24	chr1:154158800-154160800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
25	chr1:154159000-154159600	Weak transcription	Pancreas	Pancrea
26	chr1:154159000-154159600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:154159000-154159800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:154159000-154159800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:154159000-154159800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr1:154159000-154159800	Weak transcription	HSMMtube	muscle
31	chr1:154159000-154160400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:154159000-154164600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:154159000-154184400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:154159200-154160000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:154159400-154159600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:154159400-154159800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr1:154159400-154159800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:154159400-154159800	Enhancers	Small Intestine	intestine
39	chr1:154159400-154160200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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