Variant report

Variant	rs4477578
Chromosome Location	chr13:53224634-53224635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr13:53224570-53225238	PBDE	blood:	n/a	n/a
2	POLR2A	chr13:53223641-53227485	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr13:53224162-53225535	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr13:53223860-53227638	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr13:53223282-53227747	K562	blood:	n/a	n/a
6	POLR2A	chr13:53223142-53225413	GM12878	blood:	n/a	n/a
7	POLR2A	chr13:53224183-53225471	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:53191451..53193324-chr13:53224550..53227605,3	MCF-7	breast:
2	chr13:53223315..53224976-chr13:53225042..53226635,2	MCF-7	breast:
3	chr13:53199936..53201723-chr13:53223791..53226214,2	K562	blood:
4	chr13:53222599..53224957-chr13:53225140..53227476,2	MCF-7	breast:
5	chr13:53217025..53220829-chr13:53221987..53226213,6	K562	blood:

No data

Variant related genes	Relation type
SUGT1	TF binding region
ENSG00000139675	Chromatin interaction
ENSG00000165416	Chromatin interaction
ENSG00000250299	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1370081	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1898282	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2408657	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2760779	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs342771	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs342775	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs342776	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4242994	1.00[EUR][1000 genomes]
rs4242995	1.00[EUR][1000 genomes]
rs4242997	1.00[EUR][1000 genomes]
rs4338683	1.00[EUR][1000 genomes]
rs4551925	1.00[EUR][1000 genomes]
rs602525	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs619222	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6420307	1.00[EUR][1000 genomes]
rs6561680	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6561681	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs694014	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71437861	0.93[AFR][1000 genomes]
rs7324108	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7329993	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7335091	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7338913	1.00[EUR][1000 genomes]
rs7982106	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7992760	1.00[EUR][1000 genomes]
rs7994615	1.00[EUR][1000 genomes]
rs9316580	0.93[AFR][1000 genomes]
rs9316584	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9526980	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS 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	20 gene(s)	inside rSNPs	diseases
10	nsv1037189	chr13:53173013-53287060	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv541775	chr13:53173013-53287060	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
13	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 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	chr13:53192000-53224800	Weak transcription	Small Intestine	intestine
2	chr13:53192000-53225000	Weak transcription	Spleen	Spleen
3	chr13:53192200-53224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:53192200-53224800	Weak transcription	Gastric	stomach
5	chr13:53192200-53224800	Weak transcription	Pancreas	Pancrea
6	chr13:53192200-53224800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:53192400-53224800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:53192400-53224800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:53192400-53225000	Weak transcription	Right Ventricle	heart
10	chr13:53192400-53225800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr13:53192600-53224800	Weak transcription	Fetal Brain Male	brain
12	chr13:53192600-53225000	Weak transcription	Osteobl	bone
13	chr13:53192800-53224800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr13:53192800-53224800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr13:53192800-53224800	Weak transcription	Brain Angular Gyrus	brain
16	chr13:53193000-53225000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:53195000-53224800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:53198600-53225000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr13:53200200-53225000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:53203400-53225400	Weak transcription	Aorta	Aorta
21	chr13:53204200-53225000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr13:53204200-53225000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr13:53204400-53224800	Weak transcription	NHLF	lung
24	chr13:53204600-53226000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:53205200-53225000	Weak transcription	A549	lung
26	chr13:53205800-53225000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:53205800-53225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr13:53207200-53224800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:53207400-53224800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:53207400-53224800	Weak transcription	Colon Smooth Muscle	Colon
31	chr13:53214800-53224800	Weak transcription	NHDF-Ad	bronchial
32	chr13:53215400-53225000	Weak transcription	Brain Hippocampus Middle	brain
33	chr13:53215800-53225000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr13:53215800-53225000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:53216400-53224800	Weak transcription	Psoas Muscle	Psoas
36	chr13:53216400-53225000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr13:53216400-53225800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:53216600-53224800	Weak transcription	Brain Anterior Caudate	brain
39	chr13:53216600-53225000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr13:53216600-53225200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr13:53217000-53226000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr13:53218200-53225400	Weak transcription	Primary B cells from cord blood	blood
43	chr13:53218400-53225000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr13:53218600-53224800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr13:53218600-53225400	Weak transcription	Thymus	Thymus
46	chr13:53218800-53225000	Weak transcription	Primary T cells from cord blood	blood
47	chr13:53219000-53225000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr13:53219000-53225000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr13:53219200-53225200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr13:53220800-53225000	Weak transcription	Rectal Mucosa Donor 29	rectum

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