Variant report

Variant	rs550789498
Chromosome Location	chr3:136470306-136470307
allele	A/C
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	MYC	chr3:136469913-136472218	K562	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
5	HDAC2	chr3:136470095-136470654	HepG2	liver:	n/a	chr3:136470277-136470291
6	RAD21	chr3:136470158-136470646	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr3:136470163-136472420	HepG2	liver:	n/a	chr3:136472194-136472203
8	POLR2A	chr3:136470275-136470641	A549	lung:	n/a	n/a
9	POLR2A	chr3:136470033-136472148	K562	blood:	n/a	n/a
10	MXI1	chr3:136470250-136470431	K562	blood:	n/a	n/a
11	POLR2A	chr3:136468906-136472752	PBDE	blood:	n/a	n/a
12	POLR2A	chr3:136470161-136470441	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr3:136470261-136470638	K562	blood:	n/a	chr3:136470527-136470536
14	MYC	chr3:136470268-136470368	MCF-7	breast:	n/a	n/a
15	REST	chr3:136470082-136470556	HepG2	liver:	n/a	chr3:136470468-136470481
16	NFIC	chr3:136470027-136470465	HepG2	liver:	n/a	n/a
17	TBP	chr3:136468937-136470513	Hela-S3	cervix:	n/a	n/a
18	CBX3	chr3:136469910-136470492	K562	blood:	n/a	n/a
19	NFIC	chr3:136469975-136470455	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:136470008-136472743	K562	blood:	n/a	n/a
21	CHD1	chr3:136469767-136470386	H1-hESC	embryonic stem cell:	n/a	chr3:136470257-136470267
22	ZBTB7A	chr3:136470171-136470674	K562	blood:	n/a	chr3:136470490-136470501
23	POLR2A	chr3:136469954-136470581	GM12892	blood:	n/a	n/a
24	POLR2A	chr3:136470068-136472074	K562	blood:	n/a	n/a
25	POLR2A	chr3:136470254-136471088	A549	lung:	n/a	n/a
26	ARID3A	chr3:136469214-136470334	K562	blood:	n/a	n/a
27	MXI1	chr3:136470232-136472215	GM12878	blood:	n/a	chr3:136472194-136472203
28	POLR2A	chr3:136469765-136470698	K562	blood:	n/a	n/a
29	BRCA1	chr3:136470162-136470337	HepG2	liver:	n/a	n/a
30	E2F6	chr3:136470161-136471779	K562	blood:	n/a	chr3:136470996-136471004 chr3:136471395-136471404 chr3:136471423-136471432 chr3:136471392-136471404 chr3:136470730-136470739 chr3:136471673-136471685 chr3:136471396-136471403 chr3:136471377-136471386 chr3:136471454-136471463 chr3:136471396-136471403 chr3:136471395-136471403 chr3:136471544-136471553 chr3:136471396-136471403 chr3:136470259-136470268 chr3:136470474-136470484 chr3:136470537-136470547 chr3:136471393-136471404
31	GTF2F1	chr3:136470205-136470427	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:136469861-136473110	HepG2	liver:	n/a	n/a
33	CEBPB	chr3:136470156-136470433	K562	blood:	n/a	n/a
34	POLR2A	chr3:136470056-136472457	NB4	blood:	n/a	n/a
35	E2F6	chr3:136470088-136470427	A549	lung:	n/a	chr3:136470259-136470268
36	TAF1	chr3:136470145-136470469	Hela-S3	cervix:	n/a	n/a
37	MAZ	chr3:136470122-136471742	HepG2	liver:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
38	MAFK	chr3:136470206-136470360	HepG2	liver:	n/a	n/a
39	CHD1	chr3:136468963-136472242	GM12878	blood:	n/a	chr3:136470257-136470267
40	TBP	chr3:136470033-136473040	K562	blood:	n/a	n/a
41	POLR2A	chr3:136468959-136472839	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:136470097-136472391	HCT-116	colon:	n/a	n/a
43	YY1	chr3:136470241-136472039	K562	blood:	n/a	chr3:136470259-136470268 chr3:136470937-136470954 chr3:136471574-136471590 chr3:136470939-136470949 chr3:136470758-136470769 chr3:136471423-136471432 chr3:136471575-136471585 chr3:136470536-136470547 chr3:136470939-136470961 chr3:136470536-136470545 chr3:136470439-136470450 chr3:136471052-136471061 chr3:136471575-136471585 chr3:136471546-136471560 chr3:136471418-136471432 chr3:136471337-136471348 chr3:136471189-136471197 chr3:136471573-136471590
44	POLR2A	chr3:136469681-136470524	U87	brain:	n/a	n/a
45	HA-E2F1	chr3:136470049-136472207	MCF-7	breast:	n/a	chr3:136471392-136471403 chr3:136471395-136471404 chr3:136471423-136471432 chr3:136471392-136471404 chr3:136470730-136470739 chr3:136471673-136471685 chr3:136471396-136471403 chr3:136471377-136471386 chr3:136471454-136471463 chr3:136471396-136471403 chr3:136471544-136471553 chr3:136471396-136471403 chr3:136470259-136470268 chr3:136470474-136470484 chr3:136470537-136470547
46	MAX	chr3:136470032-136472084	K562	blood:	n/a	chr3:136470730-136470740 chr3:136470527-136470536 chr3:136470260-136470270 chr3:136471424-136471434
47	POLR2A	chr3:136469846-136473025	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:136470032-136472652	GM19099	blood:	n/a	n/a
49	POLR2A	chr3:136470184-136472023	A549	lung:	n/a	n/a
50	RFX5	chr3:136470230-136470406	HepG2	liver:	n/a	n/a

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	chr3:136447967..136449476-chr3:136469163..136470945,2	MCF-7	breast:
9	chr3:136470105..136470853-chr3:195269618..195270475,2	Hela-S3	cervix:
10	chr3:101567901..101568689-chr3:136470284..136471127,2	Hela-S3	cervix:
11	chr3:135912902..135916874-chr3:136469598..136473232,8	MCF-7	breast:
12	chr2:101179491..101180092-chr3:136470165..136470710,2	Hela-S3	cervix:
13	chr3:136470133..136470947-chrX:41193764..41194501,2	Hela-S3	cervix:
14	chr3:135914989..135917015-chr3:136470237..136472481,3	K562	blood:
15	chr3:136469311..136474326-chr3:136579207..136583133,7	K562	blood:
16	chr3:135912817..135916962-chr3:136469681..136473212,8	K562	blood:
17	chr1:153747489..153748173-chr3:136470178..136470949,2	Hela-S3	cervix:
18	chr3:136334079..136336516-chr3:136469054..136471144,3	MCF-7	breast:
19	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:
20	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
21	chr3:136469358..136473351-chr3:136579831..136582888,9	MCF-7	breast:
22	chr3:136468701..136470951-chr3:136535903..136538830,3	K562	blood:
23	chr1:147806325..147807312-chr3:136470105..136471009,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000261758	TF binding region
ENSG00000114054	Chromatin interaction
ENSG00000239213	Chromatin interaction
ENSG00000115539	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000215301	Chromatin interaction
ENSG00000251708	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000144802	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000168917	Chromatin interaction
ENSG00000240695	Chromatin interaction
ENSG00000184203	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000158092	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	chr3:136468200-136473000	Active TSS	A549	lung
2	chr3:136468400-136472000	Active TSS	NHDF-Ad	bronchial
3	chr3:136468400-136472200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:136468400-136472200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:136468400-136472600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:136468600-136470400	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:136468600-136471400	Active TSS	Right Atrium	heart
8	chr3:136468600-136472200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:136468800-136470400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:136468800-136472000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:136468800-136472000	Active TSS	HMEC	breast
12	chr3:136468800-136472200	Active TSS	GM12878-XiMat	blood
13	chr3:136469000-136470400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr3:136469000-136470400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:136469000-136470400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr3:136469000-136470600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr3:136469000-136471800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:136469000-136471800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:136469000-136471800	Active TSS	Thymus	Thymus
20	chr3:136469000-136471800	Active TSS	HepG2	liver
21	chr3:136469000-136472000	Active TSS	Fetal Kidney	kidney
22	chr3:136469000-136472000	Active TSS	Hela-S3	cervix
23	chr3:136469000-136472200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:136469000-136472400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:136469000-136472400	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:136469000-136472600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:136469000-136472600	Active TSS	Colonic Mucosa	Colon
28	chr3:136469200-136471800	Active TSS	Primary T cells fromperipheralblood	blood
29	chr3:136469200-136472000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:136469200-136472000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:136469200-136472000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:136469200-136472000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:136469200-136472000	Active TSS	Fetal Intestine Small	intestine
34	chr3:136469200-136472000	Active TSS	Placenta Amnion	Placenta Amnion
35	chr3:136469200-136472000	Active TSS	NHLF	lung
36	chr3:136469200-136472200	Active TSS	Brain Anterior Caudate	brain
37	chr3:136469200-136472200	Active TSS	Fetal Intestine Large	intestine
38	chr3:136469200-136472200	Active TSS	Stomach Smooth Muscle	stomach
39	chr3:136469200-136472400	Active TSS	Aorta	Aorta
40	chr3:136469200-136472400	Active TSS	Left Ventricle	heart
41	chr3:136469200-136472400	Active TSS	Ovary	ovary
42	chr3:136469200-136472400	Active TSS	Psoas Muscle	Psoas
43	chr3:136469200-136472400	Active TSS	Right Ventricle	heart
44	chr3:136469200-136473000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:136469200-136473400	Active TSS	K562	blood
46	chr3:136469400-136470400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:136469400-136470600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
48	chr3:136469400-136471800	Active TSS	Placenta	Placenta
49	chr3:136469400-136471800	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:136469400-136471800	Active TSS	NH-A	brain

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