Variant report

Variant	rs559646081
Chromosome Location	chr3:136469852-136469853
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	SMC3	chr3:136469791-136472601	Hela-S3	cervix:	n/a	chr3:136471189-136471203 chr3:136470573-136470583 chr3:136471247-136471261 chr3:136471196-136471203
2	CTCF	chr3:136469715-136472254	A549	lung:	n/a	chr3:136471189-136471202 chr3:136471247-136471260 chr3:136471240-136471261 chr3:136471189-136471202 chr3:136471187-136471205 chr3:136471511-136471524 chr3:136471246-136471262 chr3:136471188-136471204 chr3:136471245-136471263 chr3:136471182-136471203 chr3:136471682-136471695 chr3:136471190-136471200
3	TAL1	chr3:136469847-136472703	K562	blood:	n/a	chr3:136471188-136471203 chr3:136471188-136471203 chr3:136471188-136471203
4	POLR2A	chr3:136468906-136472752	PBDE	blood:	n/a	n/a
5	TBP	chr3:136468937-136470513	Hela-S3	cervix:	n/a	n/a
6	CHD1	chr3:136469767-136470386	H1-hESC	embryonic stem cell:	n/a	chr3:136470257-136470267
7	FOS	chr3:136469523-136469952	MCF10A-Er-Src	breast:	n/a	chr3:136469615-136469624 chr3:136469671-136469683
8	ARID3A	chr3:136469214-136470334	K562	blood:	n/a	n/a
9	POLR2A	chr3:136469765-136470698	K562	blood:	n/a	n/a
10	E2F4	chr3:136469260-136469873	MCF10A-Er-Src	breast:	n/a	chr3:136469293-136469302
11	CHD1	chr3:136468963-136472242	GM12878	blood:	n/a	chr3:136470257-136470267
12	POLR2A	chr3:136468959-136472839	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:136469681-136470524	U87	brain:	n/a	n/a
14	POLR2A	chr3:136469846-136473025	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr3:136469780-136472321	Hela-S3	cervix:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
16	RAD21	chr3:136469788-136470468	IMR90	lung:	n/a	n/a
17	POLR2A	chr3:136469618-136472614	IMR90	lung:	n/a	n/a
18	SMC3	chr3:136469659-136472745	SK-N-SH	brain:	n/a	chr3:136471189-136471203 chr3:136470573-136470583 chr3:136471247-136471261 chr3:136471196-136471203
19	POLR2A	chr3:136469829-136473142	SK-N-MC	brain:	n/a	n/a
20	NFIC	chr3:136469510-136471835	SK-N-SH	brain:	n/a	n/a
21	RELA	chr3:136469811-136472295	GM15510	blood:	n/a	chr3:136470402-136470411 chr3:136470402-136470411
22	MXI1	chr3:136469122-136470448	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:136469610-136472546	U87	brain:	n/a	n/a
24	RFX5	chr3:136469092-136470746	Hela-S3	cervix:	n/a	chr3:136469294-136469303
25	KAP1	chr3:136469682-136470323	U2OS	brain:	n/a	n/a
26	EP300	chr3:136469731-136470381	GM12878	blood:	n/a	chr3:136470022-136470036
27	MYC	chr3:136469753-136472047	MCF10A-Er-Src	breast:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
28	IRF1	chr3:136469440-136470477	K562	blood:	n/a	chr3:136470255-136470269
29	POLR2A	chr3:136469618-136472918	PANC-1	pancreas:	n/a	n/a
30	BCLAF1	chr3:136469738-136470649	GM12878	blood:	n/a	chr3:136470538-136470547
31	RAD21	chr3:136468997-136472564	SK-N-SH	brain:	n/a	chr3:136471510-136471523 chr3:136471185-136471204 chr3:136471188-136471201 chr3:136471511-136471525 chr3:136471245-136471257 chr3:136471189-136471203 chr3:136471513-136471527 chr3:136471247-136471261 chr3:136471243-136471262 chr3:136470751-136470764
32	MYC	chr3:136469203-136472639	K562	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
33	POLR2A	chr3:136469673-136470036	SK-N-SH	brain:	n/a	n/a
34	MXI1	chr3:136469242-136472350	IMR90	lung:	n/a	chr3:136472194-136472203
35	POLR2A	chr3:136469516-136472552	U87	brain:	n/a	n/a
36	TBL1XR1	chr3:136469779-136470259	GM12878	blood:	n/a	n/a
37	MYC	chr3:136469632-136470412	MCF10A-Er-Src	breast:	n/a	chr3:136470260-136470270
38	MAX	chr3:136469821-136472637	NB4	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
39	MAZ	chr3:136469350-136472412	IMR90	lung:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
40	MTA3	chr3:136469721-136470477	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:136469769-136472503	MCF10A-Er-Src	breast:	n/a	n/a
42	MAFK	chr3:136469653-136470331	IMR90	lung:	n/a	n/a
43	RCOR1	chr3:136469697-136472200	Hela-S3	cervix:	n/a	n/a
44	NFIC	chr3:136469799-136470579	GM12878	blood:	n/a	n/a
45	ZNF384	chr3:136469781-136470537	K562	blood:	n/a	n/a
46	POLR2A	chr3:136469795-136470649	HepG2	liver:	n/a	n/a
47	MAX	chr3:136469722-136472174	ECC-1	luminal epithelium:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
48	STAT3	chr3:136469829-136470179	MCF10A-Er-Src	breast:	n/a	n/a
49	MAFK	chr3:136469745-136470473	Hela-S3	cervix:	n/a	n/a
50	MXI1	chr3:136469517-136472913	SK-N-SH	brain:	n/a	chr3:136472194-136472203

No.	Distal block	Cell Line	Cell type
1	chr3:136466613..136474326-chr3:136579481..136583133,10	K562	blood:
2	chr3:136453394..136456450-chr3:136469548..136472199,3	K562	blood:
3	chr3:136468701..136475672-chr3:136535815..136540749,9	K562	blood:
4	chr3:136350170..136353597-chr3:136468835..136472616,3	MCF-7	breast:
5	chr11:62609047..62610004-chr3:136469655..136471390,4	Hela-S3	cervix:
6	chr3:136460807..136463236-chr3:136469569..136471141,2	MCF-7	breast:
7	chr3:135968756..135970580-chr3:136469634..136471998,2	K562	blood:
8	chr3:136208388..136211090-chr3:136467197..136470066,2	K562	blood:
9	chr3:136447967..136449476-chr3:136469163..136470945,2	MCF-7	breast:
10	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
11	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:
12	chr3:136233567..136235148-chr3:136468458..136469958,2	K562	blood:
13	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
14	chr3:136334079..136336516-chr3:136469054..136471144,3	MCF-7	breast:
15	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:
16	chr3:136469358..136473351-chr3:136579831..136582888,9	MCF-7	breast:
17	chr3:136468701..136470951-chr3:136535903..136538830,3	K562	blood:

Variant related genes	Relation type
ENSG00000261758	TF binding region
ENSG00000158092	Chromatin interaction
ENSG00000168917	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000240695	Chromatin interaction
ENSG00000251708	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3423516	chr3:136469287-136472135	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136449000-136470000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136454200-136470000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:136457400-136470000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:136458400-136470000	Weak transcription	Esophagus	oesophagus
5	chr3:136465800-136470000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:136468000-136470000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:136468200-136473000	Active TSS	A549	lung
8	chr3:136468400-136470000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:136468400-136470000	Weak transcription	Pancreas	Pancrea
10	chr3:136468400-136470000	Weak transcription	Stomach Mucosa	stomach
11	chr3:136468400-136470200	Weak transcription	Gastric	stomach
12	chr3:136468400-136472000	Active TSS	NHDF-Ad	bronchial
13	chr3:136468400-136472200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:136468400-136472200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:136468400-136472600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:136468600-136470000	Weak transcription	Lung	lung
17	chr3:136468600-136470400	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr3:136468600-136471400	Active TSS	Right Atrium	heart
19	chr3:136468600-136472200	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr3:136468800-136470000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:136468800-136470200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr3:136468800-136470400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:136468800-136472000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:136468800-136472000	Active TSS	HMEC	breast
25	chr3:136468800-136472200	Active TSS	GM12878-XiMat	blood
26	chr3:136469000-136470000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:136469000-136470000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:136469000-136470000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr3:136469000-136470000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:136469000-136470000	Flanking Active TSS	Fetal Brain Male	brain
31	chr3:136469000-136470400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr3:136469000-136470400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:136469000-136470400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:136469000-136470600	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:136469000-136471800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:136469000-136471800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:136469000-136471800	Active TSS	Thymus	Thymus
38	chr3:136469000-136471800	Active TSS	HepG2	liver
39	chr3:136469000-136472000	Active TSS	Fetal Kidney	kidney
40	chr3:136469000-136472000	Active TSS	Hela-S3	cervix
41	chr3:136469000-136472200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:136469000-136472400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:136469000-136472400	Active TSS	Fetal Muscle Trunk	muscle
44	chr3:136469000-136472600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:136469000-136472600	Active TSS	Colonic Mucosa	Colon
46	chr3:136469200-136470000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:136469200-136470000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:136469200-136470000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr3:136469200-136470000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:136469200-136470000	Weak transcription	Small Intestine	intestine

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