Variant report

Variant	rs542339738
Chromosome Location	chr10:99257987-99257988
allele	C/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	GTF2F1	chr10:99257348-99258436	Hela-S3	cervix:	n/a	n/a
2	NFIC	chr10:99257618-99258038	HepG2	liver:	n/a	n/a
3	ARID3A	chr10:99257446-99258580	HepG2	liver:	n/a	n/a
4	EP300	chr10:99257833-99258293	HepG2	liver:	n/a	n/a
5	ATF3	chr10:99257759-99258622	GM12878	blood:	n/a	chr10:99258244-99258264 chr10:99258238-99258247 chr10:99258410-99258419
6	RAD21	chr10:99257373-99258798	IMR90	lung:	n/a	chr10:99258614-99258624 chr10:99258781-99258791 chr10:99257519-99257533 chr10:99258728-99258738
7	ELF1	chr10:99257380-99258520	MCF-7	breast:	n/a	chr10:99258354-99258363
8	RFX5	chr10:99257427-99258815	Hela-S3	cervix:	n/a	n/a
9	MAZ	chr10:99257433-99259409	K562	blood:	n/a	chr10:99258254-99258265 chr10:99258920-99258930 chr10:99258255-99258264 chr10:99259189-99259199 chr10:99258671-99258681 chr10:99259326-99259336
10	NRF1	chr10:99257729-99258646	H1-hESC	embryonic stem cell:	n/a	chr10:99258007-99258016 chr10:99258238-99258247 chr10:99258197-99258208
11	POLR2A	chr10:99257433-99258866	GM18951	blood:	n/a	n/a
12	ETS1	chr10:99257950-99258219	K562	blood:	n/a	n/a
13	POLR2A	chr10:99257272-99258520	GM12878	blood:	n/a	n/a
14	MAX	chr10:99257348-99258696	H1-hESC	embryonic stem cell:	n/a	chr10:99258254-99258265 chr10:99258255-99258264 chr10:99258671-99258681
15	MXI1	chr10:99257451-99258660	K562	blood:	n/a	n/a
16	YY1	chr10:99257458-99258479	A549	lung:	n/a	chr10:99258238-99258247 chr10:99258010-99258024
17	POLR2A	chr10:99257471-99258931	HEK293	kidney:	n/a	n/a
18	ZC3H11A	chr10:99257752-99258121	K562	blood:	n/a	n/a
19	SP1	chr10:99257324-99258857	A549	lung:	n/a	chr10:99258239-99258248 chr10:99258581-99258593 chr10:99258237-99258249 chr10:99258239-99258248 chr10:99258293-99258304 chr10:99258293-99258305 chr10:99258583-99258592 chr10:99258429-99258443 chr10:99258294-99258304 chr10:99258237-99258249 chr10:99258295-99258304 chr10:99258582-99258592 chr10:99258295-99258304 chr10:99258293-99258305 chr10:99258294-99258304 chr10:99258562-99258576 chr10:99258290-99258304 chr10:99258294-99258303 chr10:99258238-99258248 chr10:99258234-99258248 chr10:99258555-99258568 chr10:99258668-99258680 chr10:99258583-99258592 chr10:99258670-99258679 chr10:99258238-99258247 chr10:99258238-99258248 chr10:99258582-99258591
20	NRF1	chr10:99257331-99258604	Hela-S3	cervix:	n/a	chr10:99258007-99258016 chr10:99258238-99258247 chr10:99258197-99258208
21	POLR2A	chr10:99257157-99259066	PFSK-1	brain:	n/a	n/a
22	USF1	chr10:99257520-99258851	SK-N-SH	brain:	n/a	chr10:99258255-99258264 chr10:99258254-99258263 chr10:99258255-99258264 chr10:99257608-99257624 chr10:99258256-99258265 chr10:99258253-99258266
23	REST	chr10:99257830-99258256	HepG2	liver:	n/a	n/a
24	POLR2A	chr10:99257369-99258670	GM15510	blood:	n/a	n/a
25	NFIC	chr10:99257347-99259530	ECC-1	luminal epithelium:	n/a	n/a
26	BRCA1	chr10:99257716-99258020	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F4	chr10:99257489-99258708	MCF10A-Er-Src	breast:	n/a	chr10:99258670-99258679 chr10:99257949-99257961 chr10:99258238-99258247
28	BHLHE40	chr10:99257292-99258845	GM12878	blood:	n/a	chr10:99258255-99258264 chr10:99258254-99258263 chr10:99258255-99258264 chr10:99257608-99257624 chr10:99258256-99258265 chr10:99258253-99258266
29	MAX	chr10:99257409-99258850	MCF-7	breast:	n/a	chr10:99258254-99258265 chr10:99258255-99258264 chr10:99258671-99258681
30	HCFC1	chr10:99257445-99258383	K562	blood:	n/a	n/a
31	PML	chr10:99257415-99258397	MCF-7	breast:	n/a	n/a
32	POU2F2	chr10:99257362-99258328	GM12878	blood:	n/a	n/a
33	ATF3	chr10:99257910-99258563	HepG2	liver:	n/a	chr10:99258244-99258264 chr10:99258238-99258247 chr10:99258410-99258419
34	EBF1	chr10:99257933-99258831	GM12878	blood:	n/a	chr10:99258221-99258230
35	MAZ	chr10:99257613-99259393	HepG2	liver:	n/a	chr10:99258254-99258265 chr10:99258920-99258930 chr10:99258255-99258264 chr10:99259189-99259199 chr10:99258671-99258681 chr10:99259326-99259336
36	POLR2A	chr10:99257503-99258166	HepG2	liver:	n/a	n/a
37	BCL3	chr10:99257417-99258085	A549	lung:	n/a	n/a
38	CEBPD	chr10:99257984-99258242	HepG2	liver:	n/a	n/a
39	MAX	chr10:99257444-99258770	Hela-S3	cervix:	n/a	chr10:99258254-99258265 chr10:99258255-99258264 chr10:99258671-99258681
40	ATF2	chr10:99257859-99258257	GM12878	blood:	n/a	n/a
41	SIN3AK20	chr10:99257467-99258430	MCF-7	breast:	n/a	n/a
42	POLR2A	chr10:99257471-99258529	K562	blood:	n/a	n/a
43	SIN3AK20	chr10:99257482-99258243	A549	lung:	n/a	n/a
44	MTA3	chr10:99257512-99258215	GM12878	blood:	n/a	n/a
45	POLR2A	chr10:99257391-99258844	Hela-S3	cervix:	n/a	n/a
46	MYBL2	chr10:99257384-99258397	HepG2	liver:	n/a	n/a
47	TAF1	chr10:99257425-99258249	GM12891	blood:	n/a	n/a
48	HMGN3	chr10:99257521-99259484	K562	blood:	n/a	n/a
49	MAX	chr10:99257406-99259409	NB4	blood:	n/a	chr10:99258254-99258265 chr10:99258920-99258930 chr10:99258255-99258264 chr10:99259189-99259199 chr10:99258671-99258681 chr10:99259326-99259336
50	POLR2A	chr10:99257160-99259048	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99256769..99258998-chr15:71406274..71408704,2	MCF-7	breast:
2	chr10:99205729..99207747-chr10:99256104..99259230,4	MCF-7	breast:
3	chr10:99257383..99259278-chr10:99348125..99351802,3	MCF-7	breast:
4	chr10:99184102..99187983-chr10:99256299..99259028,4	MCF-7	breast:
5	chr10:99226678..99229676-chr10:99256675..99258497,3	K562	blood:
6	chr10:99256761..99259494-chr10:99495841..99497583,3	K562	blood:
7	chr10:99255590..99258774-chr10:99331777..99334688,4	MCF-7	breast:
8	chr10:99257860..99258824-chr19:39109137..39109745,2	NB4	blood:
9	chr10:99255036..99258001-chr10:99391751..99393858,2	K562	blood:
10	chr1:92948945..92949798-chr10:99257544..99258444,2	NB4	blood:
11	chr10:99256903..99258777-chr10:99359333..99362265,3	MCF-7	breast:
12	chr10:99159358..99162440-chr10:99256931..99260180,3	MCF-7	breast:
13	chr10:99204416..99207741-chr10:99255231..99259773,5	K562	blood:
14	chr10:99222186..99224911-chr10:99257446..99259011,2	MCF-7	breast:
15	chr10:99186982..99190152-chr10:99256815..99259689,3	K562	blood:
16	chr10:99205621..99207743-chr10:99257584..99260294,2	MCF-7	breast:
17	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
18	chr10:99158733..99161055-chr10:99257726..99260280,2	MCF-7	breast:
19	chr10:99257419..99257994-chr19:1591863..1592383,2	Hela-S3	cervix:
20	chr10:99257811..99258591-chr7:27170109..27170609,2	NB4	blood:
21	chr10:99257277..99258845-chr10:99472952..99474913,2	MCF-7	breast:
22	chr10:99229450..99232386-chr10:99257902..99259455,2	MCF-7	breast:

Variant related genes	Relation type
UBTD1	TF binding region
ENSG00000231970	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000071655	Chromatin interaction
ENSG00000203942	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000155254	Chromatin interaction
ENSG00000155256	Chromatin interaction
ENSG00000224474	Chromatin interaction
ENSG00000197576	Chromatin interaction
ENSG00000241935	Chromatin interaction
ENSG00000165887	Chromatin interaction
ENSG00000162676	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000171160	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000052749	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3440915	chr10:99257587-99260135	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99256400-99259400	Active TSS	K562	blood
2	chr10:99256600-99258000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr10:99256600-99258000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr10:99256600-99258000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:99256800-99258000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:99256800-99258000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:99256800-99259800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr10:99256800-99260000	Active TSS	Aorta	Aorta
9	chr10:99257000-99258000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr10:99257000-99259000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:99257000-99259400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:99257000-99259400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:99257000-99259400	Active TSS	Stomach Smooth Muscle	stomach
14	chr10:99257000-99259400	Active TSS	GM12878-XiMat	blood
15	chr10:99257000-99259600	Active TSS	Fetal Muscle Leg	muscle
16	chr10:99257000-99259600	Active TSS	NHEK	skin
17	chr10:99257000-99259800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:99257000-99259800	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr10:99257000-99259800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:99257000-99259800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr10:99257000-99259800	Active TSS	A549	lung
22	chr10:99257000-99259800	Active TSS	HSMMtube	muscle
23	chr10:99257000-99259800	Active TSS	NHDF-Ad	bronchial
24	chr10:99257000-99259800	Active TSS	NHLF	lung
25	chr10:99257000-99260400	Active TSS	Brain Angular Gyrus	brain
26	chr10:99257000-99260400	Active TSS	HSMM	muscle
27	chr10:99257200-99258000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr10:99257200-99258000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr10:99257200-99258000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:99257200-99258000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr10:99257200-99258000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr10:99257200-99258000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr10:99257200-99258000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr10:99257200-99259200	Active TSS	Hela-S3	cervix
35	chr10:99257200-99259400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr10:99257200-99259400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr10:99257200-99259600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:99257200-99259600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr10:99257200-99259600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr10:99257200-99259600	Active TSS	Brain Cingulate Gyrus	brain
41	chr10:99257200-99259600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:99257200-99259800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:99257200-99259800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:99257200-99259800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:99257200-99259800	Active TSS	Muscle Satellite Cultured Cells	--
46	chr10:99257200-99259800	Active TSS	Brain Anterior Caudate	brain
47	chr10:99257200-99259800	Active TSS	Fetal Kidney	kidney
48	chr10:99257200-99259800	Active TSS	Psoas Muscle	Psoas
49	chr10:99257200-99259800	Active TSS	Right Ventricle	heart
50	chr10:99257200-99259800	Active TSS	HMEC	breast

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