Variant report

Variant	rs58279895
Chromosome Location	chr4:2937854-2937855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:230)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:230 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr4:2937112-2938144	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr4:2937697-2938068	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:2936416-2939933	GM18505	blood:	n/a	n/a
4	POLR2A	chr4:2936463-2940004	GM12891	blood:	n/a	n/a
5	SMC3	chr4:2936999-2938243	Hela-S3	cervix:	n/a	n/a
6	FOSL1	chr4:2937691-2938133	K562	blood:	n/a	chr4:2937931-2937942
7	FOS	chr4:2937660-2938188	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:2936427-2939614	Hela-S3	cervix:	n/a	n/a
9	TAL1	chr4:2937756-2938684	K562	blood:	n/a	n/a
10	JUND	chr4:2937701-2938223	K562	blood:	n/a	n/a
11	SP1	chr4:2937714-2938509	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:2935540-2939822	Hela-S3	cervix:	n/a	n/a
13	MAX	chr4:2936301-2939648	HCT-116	colon:	n/a	n/a
14	ELF1	chr4:2937616-2938172	GM12878	blood:	n/a	n/a
15	BATF	chr4:2937726-2938233	GM12878	blood:	n/a	n/a
16	GATA3	chr4:2937607-2938139	MCF-7	breast:	n/a	n/a
17	HCFC1	chr4:2936424-2938309	Hela-S3	cervix:	n/a	n/a
18	RELA	chr4:2937153-2939870	GM18505	blood:	n/a	n/a
19	MTA3	chr4:2936419-2940060	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:2936420-2939905	K562	blood:	n/a	n/a
21	POLR2A	chr4:2936475-2940008	GM12891	blood:	n/a	n/a
22	POLR2A	chr4:2937124-2940033	K562	blood:	n/a	n/a
23	RCOR1	chr4:2937669-2938129	K562	blood:	n/a	n/a
24	SIN3AK20	chr4:2936414-2939621	HCT-116	colon:	n/a	n/a
25	WRNIP1	chr4:2937435-2937966	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:2937075-2939631	H1-hESC	embryonic stem cell:	n/a	n/a
27	BCLAF1	chr4:2937706-2939670	GM12878	blood:	n/a	n/a
28	NFIC	chr4:2937695-2938668	GM12878	blood:	n/a	n/a
29	NFATC1	chr4:2936959-2939864	GM12878	blood:	n/a	n/a
30	MAZ	chr4:2937730-2938120	Hela-S3	cervix:	n/a	n/a
31	SP1	chr4:2937757-2938160	GM12878	blood:	n/a	n/a
32	JUND	chr4:2937092-2939655	HCT-116	colon:	n/a	n/a
33	NR2F2	chr4:2936909-2938256	K562	blood:	n/a	n/a
34	POLR2A	chr4:2936428-2940062	K562	blood:	n/a	n/a
35	POLR2A	chr4:2936474-2938797	IMR90	lung:	n/a	n/a
36	GATA3	chr4:2937564-2938271	MCF-7	breast:	n/a	n/a
37	POLR2A	chr4:2936942-2939390	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr4:2936392-2939634	HCT-116	colon:	n/a	n/a
39	POLR2A	chr4:2936273-2939674	MCF-7	breast:	n/a	n/a
40	FOSL1	chr4:2937740-2938231	K562	blood:	n/a	chr4:2937931-2937942
41	EGR1	chr4:2937849-2938183	K562	blood:	n/a	n/a
42	ZNF263	chr4:2936629-2937899	HEK293-T-REx	kidney:	n/a	n/a
43	TCF12	chr4:2937728-2938197	GM12878	blood:	n/a	n/a
44	CEBPD	chr4:2937614-2938202	K562	blood:	n/a	n/a
45	STAT3	chr4:2937538-2938071	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:2936425-2939503	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:2937759-2939502	K562	blood:	n/a	n/a
48	GATA2	chr4:2937582-2938177	K562	blood:	n/a	n/a
49	STAT3	chr4:2937540-2938068	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr4:2936447-2940060	GM12892	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2756410..2759745-chr4:2935120..2939466,6	K562	blood:
2	chr4:2830493..2833231-chr4:2936573..2940194,3	MCF-7	breast:
3	chr4:2937764..2938593-chr7:5569551..5570127,2	Hela-S3	cervix:
4	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
5	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
6	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:
7	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
8	chr4:2935808..2938115-chr4:3076304..3078834,3	K562	blood:
9	chr4:2744637..2750348-chr4:2934999..2939149,7	MCF-7	breast:
10	chr1:149856723..149858846-chr4:2935922..2938266,2	MCF-7	breast:
11	chr4:2756586..2759605-chr4:2935863..2938872,4	K562	blood:
12	chr4:2936565..2939326-chr4:2970679..2973500,2	K562	blood:
13	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
14	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
15	chr4:2937332..2937943-chrX:41193378..41193993,2	Hela-S3	cervix:
16	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
17	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
18	chr4:774518..776312-chr4:2935741..2938166,2	MCF-7	breast:
19	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
20	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
21	chr4:2844179..2847079-chr4:2935598..2937938,4	MCF-7	breast:
22	chr4:2937494..2938263-chrX:11129002..11129919,2	Hela-S3	cervix:
23	chr18:3447926..3450158-chr4:2936583..2939331,2	MCF-7	breast:
24	chr4:2818330..2820965-chr4:2936129..2938646,4	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2937273-2939869	ENSG00000249673
2	lnc-ADD1-1	chr4:2937273-2938617	ENSG00000249673
3	lnc-ADD1-1	chr4:2937278-2939869	NR_015453
4	lnc-ADD1-1	chr4:2937273-2938617	ENSG00000249673.2

No data

Variant related genes	Relation type
NOP14-AS1	TF binding region
MFSD10	TF binding region
ENSG00000234129	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000087266	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000004961	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000215301	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000075624	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs16843459	1.00[AMR][1000 genomes]
rs16843490	1.00[AMR][1000 genomes]
rs16843682	1.00[AMR][1000 genomes]
rs35304823	1.00[AMR][1000 genomes]
rs35983864	1.00[AMR][1000 genomes]
rs55676948	1.00[AMR][1000 genomes]
rs56315133	1.00[AMR][1000 genomes]
rs57551202	1.00[AMR][1000 genomes]
rs57960709	1.00[AMR][1000 genomes]
rs60514033	1.00[AMR][1000 genomes]
rs60745500	1.00[AMR][1000 genomes]
rs61652297	1.00[AMR][1000 genomes]
rs61747144	1.00[AMR][1000 genomes]
rs6830234	1.00[AMR][1000 genomes]
rs73792109	1.00[AMR][1000 genomes]
rs73792110	1.00[AMR][1000 genomes]
rs73792112	1.00[AMR][1000 genomes]
rs73792115	1.00[AMR][1000 genomes]
rs73792116	1.00[AMR][1000 genomes]
rs73794816	1.00[AMR][1000 genomes]
rs73794824	1.00[AMR][1000 genomes]
rs73794825	1.00[AMR][1000 genomes]
rs73794827	1.00[AMR][1000 genomes]
rs7657843	1.00[AMR][1000 genomes]
rs7676937	1.00[AMR][1000 genomes]
rs7699427	1.00[AMR][1000 genomes]
rs9686059	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2935200-2938000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:2935200-2938000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:2935400-2938000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:2936600-2939600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:2936800-2938000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:2936800-2938400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr4:2936800-2939000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr4:2937000-2938000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr4:2937000-2938000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:2937000-2938000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:2937000-2938000	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr4:2937000-2938000	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr4:2937000-2938000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr4:2937000-2938400	Flanking Active TSS	Dnd41	blood
15	chr4:2937000-2938400	Flanking Active TSS	Osteobl	bone
16	chr4:2937000-2938600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr4:2937000-2938600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr4:2937000-2938600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr4:2937000-2939000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:2937200-2938000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:2937200-2938000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr4:2937200-2938000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:2937200-2938000	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr4:2937200-2938000	Flanking Active TSS	Fetal Lung	lung
25	chr4:2937200-2938200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr4:2937200-2938200	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr4:2937200-2938400	Flanking Active TSS	K562	blood
28	chr4:2937200-2938800	Flanking Active TSS	NH-A	brain
29	chr4:2937200-2939600	Flanking Active TSS	HMEC	breast
30	chr4:2937200-2939800	Transcr. at gene 5' and 3'	NHEK	skin
31	chr4:2937400-2938000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:2937400-2938000	Enhancers	Primary B cells from cord blood	blood
33	chr4:2937400-2938000	Weak transcription	Gastric	stomach
34	chr4:2937400-2938200	Enhancers	Placenta	Placenta
35	chr4:2937400-2938400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr4:2937400-2938600	Enhancers	Spleen	Spleen
37	chr4:2937400-2938600	Flanking Active TSS	HSMM	muscle
38	chr4:2937400-2939000	Flanking Active TSS	Hela-S3	cervix
39	chr4:2937400-2939400	Weak transcription	Ovary	ovary
40	chr4:2937600-2938000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:2937600-2938000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:2937600-2938000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:2937600-2938000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:2937600-2938000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:2937600-2938000	Enhancers	Aorta	Aorta
46	chr4:2937600-2938000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr4:2937600-2938000	Enhancers	Right Atrium	heart
48	chr4:2937600-2938000	Enhancers	HSMMtube	muscle
49	chr4:2937600-2938000	Enhancers	HUVEC	blood vessel
50	chr4:2937600-2938000	Enhancers	Monocytes-CD14+_RO01746	blood

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