Variant report

Variant	rs547988316
Chromosome Location	chr3:179040549-179040550
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	CREB1	chr3:179040436-179041003	A549	lung:	n/a	n/a
2	TBL1XR1	chr3:179040404-179041594	GM12878	blood:	n/a	n/a
3	WRNIP1	chr3:179040246-179040757	GM12878	blood:	n/a	n/a
4	RCOR1	chr3:179040162-179041791	Hela-S3	cervix:	n/a	n/a
5	NFIC	chr3:179040170-179040923	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:179040275-179041705	K562	blood:	n/a	n/a
7	GATA3	chr3:179040139-179040991	T-47D	breast:	n/a	n/a
8	CTCF	chr3:179040540-179040690	AoAF	blood vessel:	n/a	n/a
9	MYC	chr3:179040489-179040935	HUVEC	blood vessel:	n/a	chr3:179040898-179040907
10	MYC	chr3:179039897-179042523	MCF10A-Er-Src	breast:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
11	HDAC2	chr3:179040153-179040967	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFF	chr3:179040535-179040806	HepG2	liver:	n/a	n/a
13	YY1	chr3:179040539-179040982	GM12891	blood:	n/a	chr3:179040972-179040981 chr3:179040861-179040872
14	MYC	chr3:179040415-179040562	MCF-7	breast:	n/a	n/a
15	YY1	chr3:179040364-179041635	ECC-1	luminal epithelium:	n/a	chr3:179041008-179041017 chr3:179041030-179041039 chr3:179041015-179041029 chr3:179041024-179041035 chr3:179040972-179040981 chr3:179040861-179040872 chr3:179041027-179041036
16	BRCA1	chr3:179040258-179040796	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:179040285-179041602	ProgFib	skin:	n/a	n/a
18	JUND	chr3:179040194-179041796	K562	blood:	n/a	chr3:179040556-179040565 chr3:179041077-179041085
19	BHLHE40	chr3:179040060-179041722	GM12878	blood:	n/a	chr3:179040974-179040990 chr3:179041029-179041045 chr3:179041288-179041304
20	POLR2A	chr3:179040158-179041832	GM12891	blood:	n/a	n/a
21	POLR2A	chr3:179040279-179041580	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr3:179040223-179041650	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:179040365-179041384	H1-hESC	embryonic stem cell:	n/a	n/a
24	IRF1	chr3:179040493-179041291	K562	blood:	n/a	n/a
25	CTCF	chr3:179040330-179041422	K562	blood:	n/a	chr3:179041292-179041305
26	POLR2A	chr3:179040298-179041839	GM15510	blood:	n/a	n/a
27	TAF1	chr3:179040417-179041679	K562	blood:	n/a	n/a
28	GTF2F1	chr3:179040327-179040919	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZBTB7A	chr3:179040527-179040875	HepG2	liver:	n/a	chr3:179040543-179040550
30	NR2F2	chr3:179040105-179041727	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:179040199-179041645	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr3:179040226-179041595	K562	blood:	n/a	chr3:179040898-179040907
33	EP300	chr3:179040458-179040953	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:179040226-179041601	HCT-116	colon:	n/a	n/a
35	POLR2A	chr3:179040193-179041727	HL-60	blood:	n/a	n/a
36	POLR2A	chr3:179040287-179041864	GM12892	blood:	n/a	n/a
37	HCFC1	chr3:179039384-179042423	Hela-S3	cervix:	n/a	n/a
38	E2F6	chr3:179040242-179041760	H1-hESC	embryonic stem cell:	n/a	chr3:179040829-179040838 chr3:179040972-179040981 chr3:179041028-179041038 chr3:179040633-179040648 chr3:179041162-179041174 chr3:179040793-179040805
39	NFIC	chr3:179040176-179041807	ECC-1	luminal epithelium:	n/a	n/a
40	SP1	chr3:179040394-179041007	A549	lung:	n/a	chr3:179040913-179040927 chr3:179040794-179040806 chr3:179040768-179040782 chr3:179040795-179040809 chr3:179040640-179040649 chr3:179040796-179040805 chr3:179040768-179040777
41	GTF2F1	chr3:179040068-179040952	K562	blood:	n/a	n/a
42	POLR2A	chr3:179040276-179041704	IMR90	lung:	n/a	n/a
43	JUND	chr3:179040449-179041025	A549	lung:	n/a	chr3:179040556-179040565
44	MAX	chr3:179040229-179042627	NB4	blood:	n/a	chr3:179042200-179042210 chr3:179042171-179042178 chr3:179042168-179042179 chr3:179040898-179040907 chr3:179042164-179042183
45	RELA	chr3:179040222-179041707	GM15510	blood:	n/a	n/a
46	KAP1	chr3:179039517-179040769	U2OS	brain:	n/a	n/a
47	CEBPB	chr3:179040057-179041934	Hela-S3	cervix:	n/a	n/a
48	EGR1	chr3:179040358-179041298	MCF-7	breast:	n/a	chr3:179040829-179040838 chr3:179040770-179040780 chr3:179041231-179041244 chr3:179040770-179040783 chr3:179040548-179040561
49	RCOR1	chr3:179039509-179040850	K562	blood:	n/a	n/a
50	POLR2A	chr3:179040199-179041827	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:178864344..178867597-chr3:179039214..179042429,8	K562	blood:
2	chr3:178978041..178980864-chr3:179039699..179042008,3	K562	blood:
3	chr3:178977469..178980839-chr3:179038593..179042214,6	K562	blood:
4	chr3:178864924..178867052-chr3:179038904..179040552,2	MCF-7	breast:
5	chr3:179039679..179043417-chr3:179063023..179066951,5	K562	blood:
6	chr3:179040252..179043387-chr3:179064355..179067344,4	MCF-7	breast:
7	chr3:178787120..178791261-chr3:179039253..179041998,3	K562	blood:
8	chr3:179040254..179044115-chr3:179063916..179068626,6	K562	blood:
9	chr3:179037868..179043452-chr3:179279283..179282534,12	K562	blood:
10	chr3:179039368..179041573-chr3:179044284..179046543,4	MCF-7	breast:
11	chr3:179037735..179042391-chr3:179277921..179283824,9	MCF-7	breast:
12	chr3:179039334..179043117-chr3:179061578..179071936,16	MCF-7	breast:
13	chr3:179040074..179043948-chr3:179167085..179170222,5	K562	blood:
14	chr3:179039352..179043378-chr3:179279283..179282999,10	K562	blood:
15	chr3:179040175..179040953-chr3:179065036..179065918,2	MCF-7	breast:
16	chr3:179039610..179042933-chr3:179054240..179057497,4	MCF-7	breast:
17	chr3:178977431..178979193-chr3:179039095..179041437,2	MCF-7	breast:
18	chr3:178788412..178790187-chr3:179039067..179041157,2	MCF-7	breast:
19	chr3:178977854..178979821-chr3:179040251..179043018,2	MCF-7	breast:
20	chr3:178865407..178867483-chr3:179039203..179041371,3	K562	blood:
21	chr3:179040206..179042939-chr3:179043914..179045418,3	MCF-7	breast:
22	chr3:179031470..179034268-chr3:179038646..179040748,3	K562	blood:
23	chr3:178787618..178789818-chr3:179039518..179042108,2	K562	blood:
24	chr3:178787982..178790546-chr3:179037129..179041546,5	MCF-7	breast:
25	chr19:12901967..12902813-chr3:179040341..179041276,2	Hela-S3	cervix:
26	chr3:179039445..179042481-chr3:179045775..179048078,4	MCF-7	breast:
27	chr3:178864492..178868931-chr3:179039553..179043493,6	MCF-7	breast:
28	chr3:179039914..179042763-chr3:179093091..179095772,2	K562	blood:

Variant related genes	Relation type
ZNF639	TF binding region
ENSG00000171109	Chromatin interaction
ENSG00000229102	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000171121	Chromatin interaction
ENSG00000273190	Chromatin interaction
ENSG00000240429	Chromatin interaction
ENSG00000121879	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000239255	Chromatin interaction
ENSG00000114450	Chromatin interaction
ENSG00000172667	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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	35 gene(s)	inside rSNPs	diseases
11	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	esv3409455	chr3:179040008-179042256	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 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	chr3:179038800-179042200	Active TSS	NHLF	lung
2	chr3:179038800-179042800	Active TSS	Ovary	ovary
3	chr3:179039000-179040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:179039000-179040600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:179039000-179040600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:179039000-179042400	Active TSS	Right Atrium	heart
7	chr3:179039000-179043200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:179039200-179040600	Flanking Active TSS	HUVEC	blood vessel
9	chr3:179039200-179040600	Flanking Active TSS	K562	blood
10	chr3:179039200-179040600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:179039200-179042600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:179039200-179042600	Active TSS	Colonic Mucosa	Colon
13	chr3:179039200-179042800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:179039400-179040600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr3:179039400-179040600	Flanking Active TSS	GM12878-XiMat	blood
16	chr3:179039400-179041200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:179039600-179040600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr3:179039600-179040600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:179039600-179040600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr3:179039600-179040600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr3:179039600-179040600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr3:179039600-179040600	Flanking Active TSS	HMEC	breast
23	chr3:179039600-179040600	Flanking Active TSS	NHEK	skin
24	chr3:179039600-179041800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:179039800-179040600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr3:179039800-179040600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:179039800-179040600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:179039800-179040600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr3:179039800-179040600	ZNF genes & repeats	Fetal Brain Male	brain
30	chr3:179039800-179040600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr3:179039800-179042800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:179040000-179040600	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr3:179040000-179040600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr3:179040000-179040600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:179040000-179040600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr3:179040000-179040600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr3:179040000-179040600	Flanking Active TSS	Dnd41	blood
38	chr3:179040000-179041200	Active TSS	Brain Germinal Matrix	brain
39	chr3:179040000-179041800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:179040000-179042000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:179040000-179042200	Active TSS	Brain Angular Gyrus	brain
42	chr3:179040000-179042200	Active TSS	Colon Smooth Muscle	Colon
43	chr3:179040000-179042200	Active TSS	Fetal Intestine Large	intestine
44	chr3:179040000-179042200	Active TSS	Psoas Muscle	Psoas
45	chr3:179040000-179042400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:179040000-179042400	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:179040000-179042400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:179040000-179042400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:179040000-179042400	Active TSS	Right Ventricle	heart
50	chr3:179040000-179042600	Active TSS	H9 Cell Line	embryonic stem cell

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