Variant report

Variant	rs28409877
Chromosome Location	chr8:62625931-62625932
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	POLR2A	chr8:62624043-62628324	U87	brain:	n/a	n/a
2	POLR2A	chr8:62620749-62628224	U87	brain:	n/a	n/a
3	BCL3	chr8:62622937-62626728	A549	lung:	n/a	chr8:62622975-62622984 chr8:62623067-62623076 chr8:62626676-62626685
4	PBX3	chr8:62625573-62626292	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr8:62625686-62626233	SK-N-SH	brain:	n/a	chr8:62625945-62625954
6	POLR2A	chr8:62621167-62627994	A549	lung:	n/a	n/a
7	GATA3	chr8:62625476-62626491	SK-N-SH	brain:	n/a	n/a
8	STAT3	chr8:62625615-62626229	MCF10A-Er-Src	breast:	n/a	chr8:62625731-62625739
9	NFIC	chr8:62625493-62626412	SK-N-SH	brain:	n/a	n/a
10	MAX	chr8:62625682-62626385	SK-N-SH	brain:	n/a	chr8:62626030-62626046
11	MXI1	chr8:62624733-62626441	Hela-S3	cervix:	n/a	n/a
12	TEAD4	chr8:62625661-62626332	SK-N-SH	brain:	n/a	chr8:62626030-62626039
13	FOS	chr8:62625759-62626254	MCF10A-Er-Src	breast:	n/a	chr8:62625945-62625954
14	FOSL2	chr8:62625549-62626415	SK-N-SH	brain:	n/a	chr8:62626361-62626370 chr8:62625945-62625954
15	POLR2A	chr8:62625735-62626382	HUVEC	blood vessel:	n/a	n/a
16	RXRA	chr8:62625717-62626389	SK-N-SH	brain:	n/a	chr8:62626169-62626183
17	TEAD4	chr8:62625563-62626369	SK-N-SH	brain:	n/a	chr8:62626030-62626039
18	MAZ	chr8:62625218-62628133	IMR90	lung:	n/a	chr8:62627889-62627896 chr8:62627481-62627497 chr8:62626030-62626046 chr8:62627481-62627490 chr8:62627887-62627898 chr8:62627478-62627488 chr8:62627478-62627489 chr8:62627888-62627897 chr8:62627886-62627899 chr8:62627887-62627898 chr8:62627888-62627897 chr8:62627887-62627898 chr8:62627889-62627898 chr8:62627887-62627897
19	MAFK	chr8:62624238-62626280	Hela-S3	cervix:	n/a	n/a
20	SMC3	chr8:62624603-62628007	Hela-S3	cervix:	n/a	n/a
21	FOS	chr8:62625759-62626245	MCF10A-Er-Src	breast:	n/a	chr8:62625945-62625954
22	MXI1	chr8:62625593-62628121	SK-N-SH	brain:	n/a	chr8:62627478-62627487 chr8:62627889-62627898
23	FOS	chr8:62625813-62626221	MCF10A-Er-Src	breast:	n/a	chr8:62625945-62625954
24	TCF12	chr8:62625213-62627783	SK-N-SH	brain:	n/a	n/a
25	JUND	chr8:62625559-62626388	SK-N-SH	brain:	n/a	chr8:62626361-62626370 chr8:62625945-62625954
26	EP300	chr8:62625539-62626800	SK-N-SH	brain:	n/a	chr8:62626370-62626379 chr8:62625613-62625627
27	TCF12	chr8:62622969-62628409	A549	lung:	n/a	n/a
28	POLR2A	chr8:62624655-62628169	Hela-S3	cervix:	n/a	n/a
29	EP300	chr8:62624553-62626265	Hela-S3	cervix:	n/a	chr8:62625613-62625627 chr8:62625013-62625021
30	FOS	chr8:62625745-62626251	HUVEC	blood vessel:	n/a	chr8:62625945-62625954
31	MYC	chr8:62625870-62626245	MCF10A-Er-Src	breast:	n/a	chr8:62626030-62626046
32	STAT3	chr8:62625806-62626193	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr8:62624324-62628038	MCF10A-Er-Src	breast:	n/a	n/a
34	TCF7L2	chr8:62625701-62628160	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr8:62625828-62628132	HepG2	liver:	n/a	n/a
36	CEBPB	chr8:62625829-62626480	Hela-S3	cervix:	n/a	chr8:62626279-62626292
37	FOSL2	chr8:62624509-62626584	A549	lung:	n/a	chr8:62626361-62626370 chr8:62625945-62625954 chr8:62625013-62625022
38	SIX5	chr8:62622210-62626661	A549	lung:	n/a	chr8:62624442-62624451
39	TBP	chr8:62624597-62626541	Hela-S3	cervix:	n/a	n/a
40	REST	chr8:62624489-62626250	A549	lung:	n/a	n/a
41	CEBPB	chr8:62625687-62626655	A549	lung:	n/a	chr8:62626279-62626292
42	POLR2A	chr8:62625735-62626271	SK-N-SH	brain:	n/a	n/a
43	PBX3	chr8:62625685-62626354	SK-N-SH	brain:	n/a	n/a
44	SP1	chr8:62624276-62628263	A549	lung:	n/a	chr8:62627211-62627221 chr8:62626675-62626687 chr8:62625318-62625339 chr8:62627190-62627200 chr8:62626804-62626813 chr8:62627210-62627221 chr8:62627189-62627201 chr8:62627293-62627302 chr8:62627211-62627221 chr8:62627189-62627201 chr8:62628176-62628190 chr8:62627292-62627301 chr8:62626803-62626815 chr8:62626352-62626366 chr8:62626805-62626814 chr8:62627210-62627222 chr8:62627212-62627221 chr8:62627211-62627220 chr8:62627292-62627301 chr8:62626804-62626813 chr8:62627210-62627222 chr8:62627291-62627303 chr8:62627190-62627200 chr8:62627211-62627220 chr8:62626359-62626373
45	POLR2A	chr8:62625327-62626041	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr8:62625921-62626249	ProgFib	skin:	n/a	n/a
47	MAX	chr8:62624407-62628343	A549	lung:	n/a	chr8:62627889-62627896 chr8:62627481-62627497 chr8:62626030-62626046 chr8:62627481-62627490 chr8:62627887-62627898 chr8:62627478-62627488 chr8:62627478-62627489 chr8:62627888-62627897 chr8:62627886-62627899 chr8:62627887-62627898 chr8:62627888-62627897 chr8:62627887-62627898 chr8:62627889-62627898 chr8:62627887-62627897
48	POLR2A	chr8:62624376-62628379	Hela-S3	cervix:	n/a	n/a
49	EP300	chr8:62622946-62628108	A549	lung:	n/a	chr8:62626370-62626379 chr8:62627005-62627021 chr8:62627011-62627027 chr8:62624213-62624227 chr8:62624029-62624043 chr8:62625613-62625627 chr8:62623823-62623833 chr8:62623751-62623761 chr8:62625013-62625021 chr8:62623269-62623283 chr8:62627288-62627304 chr8:62627012-62627028 chr8:62627697-62627706 chr8:62624040-62624054 chr8:62627488-62627504
50	ARID3A	chr8:62624117-62626070	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:62560140..62569925-chr8:62619825..62628019,19	K562	blood:
2	chr8:62625715..62628343-chr8:63949746..63952148,2	MCF-7	breast:
3	chr8:62612675..62615533-chr8:62623174..62625946,2	MCF-7	breast:
4	chr8:62618042..62628934-chr8:62666240..62683608,38	K562	blood:
5	chr8:62623830..62626750-chr8:62657804..62660228,2	K562	blood:
6	chr8:62543072..62544840-chr8:62625541..62627950,2	K562	blood:
7	chr8:62625349..62627076-chr8:62628888..62631285,2	MCF-7	breast:
8	chr8:62608231..62611173-chr8:62624445..62626992,3	K562	blood:
9	chr8:62550051..62552995-chr8:62624567..62627548,2	MCF-7	breast:
10	chr8:62625464..62627946-chr8:62695567..62698459,4	MCF-7	breast:
11	chr8:62590920..62593781-chr8:62625568..62627166,2	MCF-7	breast:
12	chr8:62619459..62621551-chr8:62623294..62626246,2	MCF-7	breast:
13	chr8:62624564..62626799-chr8:62720557..62722596,2	K562	blood:
14	chr11:65273377..65274372-chr8:62625380..62626007,2	Hela-S3	cervix:
15	chr8:62597423..62607954-chr8:62618870..62628159,21	K562	blood:

Variant related genes	Relation type
MIR4470	TF binding region
ENSG00000254119	Chromatin interaction
ENSG00000137563	Chromatin interaction
ENSG00000251127	Chromatin interaction
ENSG00000222898	Chromatin interaction
ENSG00000198363	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10099866	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10108427	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2350925	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4272369	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4377960	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4446731	0.81[AMR][1000 genomes]
rs6990099	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7015043	0.80[AMR][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	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv932198	chr8:62336705-62914562	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2761430	chr8:62517980-62873803	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1015216	chr8:62517980-62873803	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62613000-62626400	Weak transcription	Lung	lung
2	chr8:62622200-62626200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:62622200-62626200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr8:62622200-62626200	Weak transcription	Pancreas	Pancrea
5	chr8:62622200-62626400	Weak transcription	Gastric	stomach
6	chr8:62622400-62626000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr8:62622400-62627800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:62622800-62627600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr8:62623000-62626000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr8:62623000-62627800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:62623200-62626200	Weak transcription	Small Intestine	intestine
12	chr8:62623200-62627400	Active TSS	NHLF	lung
13	chr8:62623200-62627600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:62623200-62627600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr8:62623400-62626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr8:62623600-62627600	Active TSS	Hela-S3	cervix
17	chr8:62623600-62627600	Active TSS	NHDF-Ad	bronchial
18	chr8:62623600-62627800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr8:62623800-62627400	Active TSS	K562	blood
20	chr8:62624000-62627200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:62624000-62627400	Active TSS	HMEC	breast
22	chr8:62624000-62627600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:62624000-62627800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr8:62624200-62626000	Flanking Active TSS	HUVEC	blood vessel
25	chr8:62624200-62626200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr8:62624200-62626200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:62624200-62626200	Transcr. at gene 5' and 3'	A549	lung
28	chr8:62624200-62626400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr8:62624200-62626600	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr8:62624200-62627600	Active TSS	HSMMtube	muscle
31	chr8:62624400-62626000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr8:62624400-62626000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr8:62624400-62626200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr8:62624400-62627400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr8:62624400-62627400	Active TSS	HSMM	muscle
36	chr8:62624400-62627600	Active TSS	Brain Cingulate Gyrus	brain
37	chr8:62624400-62627600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr8:62624400-62627600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:62624400-62627600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr8:62624400-62627600	Active TSS	Fetal Intestine Large	intestine
41	chr8:62624400-62627600	Active TSS	Fetal Stomach	stomach
42	chr8:62624400-62627600	Active TSS	Osteobl	bone
43	chr8:62624600-62626200	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr8:62624600-62626400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr8:62624600-62627400	Active TSS	Fetal Thymus	thymus
46	chr8:62624600-62627600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr8:62624600-62627600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:62624600-62627600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr8:62624600-62627600	Active TSS	Brain Angular Gyrus	brain
50	chr8:62624600-62627600	Active TSS	Sigmoid Colon	Sigmoid Colon

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