Variant report

Variant	rs553208774
Chromosome Location	chr4:2964586-2964587
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	MAX	chr4:2964486-2965973	MCF-7	breast:	n/a	chr4:2965876-2965886 chr4:2965246-2965255
2	MXI1	chr4:2964181-2965562	Hela-S3	cervix:	n/a	n/a
3	CREB1	chr4:2964414-2965875	HepG2	liver:	n/a	n/a
4	MAX	chr4:2964512-2965880	K562	blood:	n/a	chr4:2965246-2965255
5	JUND	chr4:2964482-2964608	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF7L2	chr4:2964390-2965769	HCT-116	colon:	n/a	n/a
7	POLR2A	chr4:2964479-2966046	MCF-7	breast:	n/a	n/a
8	HDAC2	chr4:2964336-2965832	HepG2	liver:	n/a	chr4:2965475-2965484
9	POLR2A	chr4:2964496-2965592	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr4:2964555-2965848	GM18526	blood:	n/a	n/a
11	POLR2A	chr4:2964557-2965566	K562	blood:	n/a	n/a
12	UBTF	chr4:2963139-2966263	K562	blood:	n/a	n/a
13	POLR2A	chr4:2964403-2965983	H1-neurons	neurons:	n/a	n/a
14	GTF2F1	chr4:2964448-2965327	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB7A	chr4:2964413-2964929	K562	blood:	n/a	n/a
16	MAX	chr4:2963092-2966134	NB4	blood:	n/a	chr4:2965876-2965886 chr4:2965246-2965255
17	JUND	chr4:2964492-2965544	K562	blood:	n/a	n/a
18	PML	chr4:2963466-2965945	GM12878	blood:	n/a	n/a
19	ZBTB33	chr4:2964382-2965560	SK-N-SH	brain:	n/a	chr4:2965144-2965154 chr4:2965143-2965152 chr4:2964662-2964671 chr4:2965141-2965156 chr4:2965165-2965180
20	BRCA1	chr4:2964483-2965545	Hela-S3	cervix:	n/a	chr4:2965143-2965152 chr4:2965170-2965179
21	POLR2A	chr4:2964441-2965251	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr4:2964401-2965641	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr4:2964407-2965960	ECC-1	luminal epithelium:	n/a	n/a
24	ZBTB33	chr4:2964359-2965615	A549	lung:	n/a	chr4:2965144-2965154 chr4:2965143-2965152 chr4:2964662-2964671 chr4:2965141-2965156 chr4:2965165-2965180
25	ZBTB7A	chr4:2964476-2965931	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:2964449-2965951	GM18505	blood:	n/a	n/a
27	POLR2A	chr4:2964476-2965264	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr4:2963047-2966632	MCF10A-Er-Src	breast:	n/a	n/a
29	BHLHE40	chr4:2964504-2965743	GM12878	blood:	n/a	chr4:2965049-2965065
30	YY1	chr4:2964561-2965880	ECC-1	luminal epithelium:	n/a	chr4:2964581-2964590 chr4:2965525-2965536 chr4:2965858-2965872 chr4:2965311-2965320 chr4:2965305-2965319 chr4:2965055-2965066 chr4:2965560-2965574 chr4:2965308-2965317 chr4:2965451-2965462 chr4:2965252-2965261
31	E2F6	chr4:2964500-2966001	K562	blood:	n/a	chr4:2965188-2965197 chr4:2965861-2965871
32	POLR2A	chr4:2964420-2965515	U87	brain:	n/a	n/a
33	BHLHE40	chr4:2964523-2965419	HepG2	liver:	n/a	chr4:2965049-2965065
34	POLR2A	chr4:2964467-2965236	GM12891	blood:	n/a	n/a
35	MAX	chr4:2964419-2965920	HepG2	liver:	n/a	chr4:2965876-2965886 chr4:2965246-2965255
36	MAFK	chr4:2964506-2964731	K562	blood:	n/a	n/a
37	POLR2A	chr4:2964431-2965376	H1-hESC	embryonic stem cell:	n/a	n/a
38	JUN	chr4:2963038-2966039	K562	blood:	n/a	chr4:2965875-2965884
39	MYC	chr4:2964506-2965837	MCF10A-Er-Src	breast:	n/a	chr4:2965246-2965255
40	HCFC1	chr4:2964492-2965859	K562	blood:	n/a	n/a
41	POLR2A	chr4:2964322-2965316	GM12878	blood:	n/a	n/a
42	GABPA	chr4:2964436-2965844	K562	blood:	n/a	chr4:2965188-2965197
43	MAX	chr4:2964577-2965444	A549	lung:	n/a	chr4:2965246-2965255
44	POLR2A	chr4:2964434-2965914	GM19099	blood:	n/a	n/a
45	POLR2A	chr4:2964414-2965567	U87	brain:	n/a	n/a
46	GTF2F1	chr4:2964578-2964789	Hela-S3	cervix:	n/a	n/a
47	MAX	chr4:2964314-2965940	A549	lung:	n/a	chr4:2965876-2965886 chr4:2965246-2965255
48	POLR2A	chr4:2964469-2965695	Hela-S3	cervix:	n/a	n/a
49	MYC	chr4:2964551-2965830	MCF-7	breast:	n/a	chr4:2965246-2965255
50	REST	chr4:2964401-2966434	H1-neurons	neurons:	n/a	chr4:2966040-2966053 chr4:2965157-2965171 chr4:2965686-2965699 chr4:2964683-2964701

No.	Distal block	Cell Line	Cell type
1	chr4:2935142..2937747-chr4:2962615..2966345,4	MCF-7	breast:
2	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
3	chr4:1857657..1859808-chr4:2963800..2965708,2	MCF-7	breast:
4	chr4:2756517..2759780-chr4:2963075..2966456,5	K562	blood:
5	chr4:2916201..2917764-chr4:2963610..2965346,2	K562	blood:
6	chr4:2948388..2950164-chr4:2962609..2964597,2	MCF-7	breast:
7	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
8	chr4:2963409..2964972-chr4:2976613..2978274,2	MCF-7	breast:
9	chr4:2756517..2759604-chr4:2963075..2966301,5	K562	blood:
10	chr4:2963799..2967429-chr4:2967585..2973552,6	K562	blood:
11	chr4:2845175..2847151-chr4:2963481..2966387,2	MCF-7	breast:

Variant related genes	Relation type
GRK4	TF binding region
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000168924	Chromatin interaction
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000251075	Chromatin interaction
ENSG00000125388	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	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
5	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1014013	chr4:2959876-3009507	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv536999	chr4:2959876-3009507	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv1003528	chr4:2964261-3011568	Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv537000	chr4:2964261-3011568	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	esv3406626	chr4:2964379-2966927	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 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	chr4:2963000-2964600	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr4:2963000-2964600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr4:2963000-2964600	Flanking Active TSS	Duodenum Mucosa	Duodenum
4	chr4:2963000-2964600	Flanking Active TSS	HUVEC	blood vessel
5	chr4:2963000-2964800	Flanking Active TSS	Liver	Liver
6	chr4:2963000-2965200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:2963000-2965400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:2963000-2966400	Active TSS	Psoas Muscle	Psoas
9	chr4:2963200-2964600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:2963200-2964600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:2963200-2964600	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr4:2963200-2964600	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr4:2963200-2964600	Flanking Active TSS	Fetal Brain Female	brain
14	chr4:2963200-2964800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr4:2963200-2964800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr4:2963200-2964800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr4:2963200-2964800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr4:2963200-2965000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr4:2963200-2965000	Flanking Active TSS	Placenta	Placenta
20	chr4:2963200-2965000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr4:2963200-2965200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:2963200-2965800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr4:2963200-2966000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr4:2963200-2966200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr4:2963200-2966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:2963400-2964600	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr4:2963400-2965000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr4:2963400-2965800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:2963400-2966000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr4:2963400-2966400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr4:2963600-2964800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:2963600-2965000	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr4:2963600-2965800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:2963600-2965800	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:2963600-2966000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:2963600-2966200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:2963600-2966400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:2963800-2964600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:2963800-2964800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr4:2963800-2965000	Active TSS	Right Atrium	heart
41	chr4:2963800-2965800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:2963800-2966000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:2963800-2966000	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr4:2963800-2966000	Active TSS	Esophagus	oesophagus
45	chr4:2963800-2966000	Active TSS	Fetal Intestine Large	intestine
46	chr4:2963800-2966000	Active TSS	Gastric	stomach
47	chr4:2963800-2966000	Active TSS	GM12878-XiMat	blood
48	chr4:2963800-2966000	Active TSS	HepG2	liver
49	chr4:2963800-2966200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:2963800-2966200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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