Variant report

Variant	rs28465300
Chromosome Location	chr8:125486323-125486324
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	HCFC1	chr8:125485176-125489186	Hela-S3	cervix:	n/a	n/a
2	SRF	chr8:125486308-125487928	MCF-7	breast:	n/a	chr8:125487199-125487209
3	POLR2A	chr8:125486247-125487957	HL-60	blood:	n/a	n/a
4	POLR2A	chr8:125485747-125488054	IMR90	lung:	n/a	n/a
5	NRF1	chr8:125485862-125487129	Hela-S3	cervix:	n/a	chr8:125487056-125487065 chr8:125486821-125486830 chr8:125486819-125486830 chr8:125486819-125486830 chr8:125486819-125486828
6	POLR2A	chr8:125485952-125488016	K562	blood:	n/a	n/a
7	WRNIP1	chr8:125486089-125487101	GM12878	blood:	n/a	n/a
8	MYC	chr8:125485786-125488002	K562	blood:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
9	MYC	chr8:125485873-125487779	K562	blood:	n/a	chr8:125487056-125487066 chr8:125486876-125486885
10	POLR2A	chr8:125485774-125488828	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr8:125486308-125486583	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYC	chr8:125485257-125487115	MCF10A-Er-Src	breast:	n/a	chr8:125487056-125487066 chr8:125486876-125486885
13	RELA	chr8:125486045-125488107	GM10847	blood:	n/a	n/a
14	CREB1	chr8:125486317-125487296	ECC-1	luminal epithelium:	n/a	chr8:125486892-125486905
15	POLR2A	chr8:125485124-125488693	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr8:125486234-125487716	NB4	blood:	n/a	n/a
17	MAX	chr8:125486236-125487971	A549	lung:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
18	SIN3A	chr8:125486091-125488880	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD1	chr8:125486183-125487176	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr8:125486009-125488915	H1-neurons	neurons:	n/a	chr8:125487587-125487597
21	TAF1	chr8:125486202-125487983	H1-neurons	neurons:	n/a	n/a
22	CBX3	chr8:125486245-125487243	K562	blood:	n/a	n/a
23	SMARCB1	chr8:125486277-125488006	Hela-S3	cervix:	n/a	n/a
24	CHD1	chr8:125486196-125489079	GM12878	blood:	n/a	n/a
25	POLR2A	chr8:125486192-125487903	GM12892	blood:	n/a	n/a
26	GABPA	chr8:125486239-125488095	MCF-7	breast:	n/a	chr8:125487201-125487210 chr8:125487056-125487065 chr8:125486821-125486830 chr8:125486819-125486830 chr8:125486819-125486828
27	POLR2A	chr8:125486160-125487505	U87	brain:	n/a	n/a
28	POLR2A	chr8:125486019-125487991	GM19193	blood:	n/a	n/a
29	POLR2A	chr8:125486071-125488148	GM12878	blood:	n/a	n/a
30	EP300	chr8:125486169-125487653	ECC-1	luminal epithelium:	n/a	chr8:125487201-125487210
31	YY1	chr8:125486271-125487822	ECC-1	luminal epithelium:	n/a	chr8:125487050-125487064 chr8:125487056-125487070 chr8:125487030-125487052 chr8:125487204-125487213
32	E2F6	chr8:125486265-125487965	K562	blood:	n/a	chr8:125487056-125487065 chr8:125486820-125486829 chr8:125487204-125487213
33	MAZ	chr8:125486316-125488031	Hela-S3	cervix:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
34	RCOR1	chr8:125486291-125487901	K562	blood:	n/a	n/a
35	JUN	chr8:125486154-125489145	K562	blood:	n/a	chr8:125486890-125486903 chr8:125487589-125487598
36	ELK1	chr8:125485734-125487342	Hela-S3	cervix:	n/a	n/a
37	TAF1	chr8:125486013-125487663	PFSK-1	brain:	n/a	n/a
38	REST	chr8:125486269-125487264	A549	lung:	n/a	n/a
39	POLR2A	chr8:125486255-125487979	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr8:125485865-125487916	Hela-S3	cervix:	n/a	chr8:125487056-125487066 chr8:125486876-125486885
41	POLR2A	chr8:125486124-125487967	GM12892	blood:	n/a	n/a
42	POLR2A	chr8:125486184-125487869	GM12891	blood:	n/a	n/a
43	NR2F2	chr8:125485964-125488186	MCF-7	breast:	n/a	n/a
44	NRF1	chr8:125485857-125487796	SK-N-SH	brain:	n/a	chr8:125487201-125487210 chr8:125487056-125487065 chr8:125486821-125486830 chr8:125486819-125486830 chr8:125486819-125486830 chr8:125486819-125486828
45	ARID3A	chr8:125485691-125487043	K562	blood:	n/a	n/a
46	POLR2A	chr8:125486016-125488152	GM12878	blood:	n/a	n/a
47	MAX	chr8:125485977-125488120	MCF-7	breast:	n/a	chr8:125487056-125487066 chr8:125486876-125486885 chr8:125487912-125487921
48	PML	chr8:125486076-125488002	K562	blood:	n/a	n/a
49	MXI1	chr8:125485872-125488618	Hela-S3	cervix:	n/a	chr8:125486870-125486885
50	POLR2A	chr8:125485665-125487935	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125482386..125490832-chr8:125532319..125553620,55	MCF-7	breast:
2	chr8:125459763..125466594-chr8:125480347..125488760,16	K562	blood:
3	chr8:125485961..125487605-chr8:126008959..126010729,2	MCF-7	breast:
4	chr8:125484053..125491713-chr8:125548138..125554442,21	K562	blood:
5	chr19:14529783..14530580-chr8:125485924..125486888,2	Hela-S3	cervix:
6	chr8:125485971..125490407-chr8:125553790..125556730,4	MCF-7	breast:
7	chr8:124407395..124409039-chr8:125486191..125487874,2	MCF-7	breast:
8	chr8:125485694..125488622-chr8:125558773..125560275,2	MCF-7	breast:
9	chr8:125484651..125489587-chr8:125535041..125543731,11	K562	blood:
10	chr8:125459763..125466513-chr8:125482159..125488968,22	K562	blood:
11	chr13:27997218..27999271-chr8:125486263..125488862,2	MCF-7	breast:
12	chr8:125483604..125491110-chr8:125548591..125554086,23	K562	blood:
13	chr8:125485539..125488439-chr8:125531952..125535064,5	MCF-7	breast:
14	chr17:56736071..56736876-chr8:125486151..125486853,2	Hela-S3	cervix:
15	chr13:110438846..110439621-chr8:125485961..125486658,2	Hela-S3	cervix:
16	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
17	chr14:104181470..104182117-chr8:125486026..125486841,2	Hela-S3	cervix:
18	chr1:116914305..116915883-chr8:125485608..125487551,2	MCF-7	breast:
19	chr8:125484977..125488762-chr8:125516872..125524765,8	MCF-7	breast:
20	chr3:49202004..49204374-chr8:125485548..125487898,2	MCF-7	breast:
21	chr12:120729389..120729935-chr8:125486270..125487096,2	NB4	blood:
22	chr8:125484651..125486969-chr8:125535041..125537083,3	K562	blood:
23	chr8:125484298..125489708-chr8:125549185..125553061,9	MCF-7	breast:
24	chr8:125485755..125491202-chr8:125535208..125540184,8	MCF-7	breast:
25	chr8:125458285..125469406-chr8:125482519..125490004,41	MCF-7	breast:
26	chr10:76993820..76995624-chr8:125485040..125487047,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TATDN1-1	chr8:125485051-125486817	ENSG00000245149
2	lnc-TATDN1-1	chr8:125484548-125487007	NONHSAT128586

Variant related genes	Relation type
RNF139	TF binding region
ENSG00000123136	Chromatin interaction
ENSG00000165644	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000156802	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000122034	Chromatin interaction
ENSG00000185950	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000163399	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000126215	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10092621	1.00[AFR][1000 genomes]
rs10097047	1.00[AFR][1000 genomes]
rs10112004	1.00[AFR][1000 genomes]
rs10481074	1.00[AFR][1000 genomes]
rs10481075	1.00[AFR][1000 genomes]
rs28403108	1.00[AFR][1000 genomes]
rs28414531	1.00[AFR][1000 genomes]
rs28446984	1.00[AFR][1000 genomes]
rs28577958	1.00[AFR][1000 genomes]
rs28696093	1.00[AFR][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	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
4	esv3339866	chr8:125485996-125488544	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 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	chr8:125484000-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:125484200-125488600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:125484200-125488600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:125484200-125488800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:125484200-125488800	Active TSS	HSMM	muscle
6	chr8:125484200-125489200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr8:125484200-125489400	Active TSS	K562	blood
8	chr8:125484400-125488400	Active TSS	Muscle Satellite Cultured Cells	--
9	chr8:125484400-125488800	Active TSS	NHLF	lung
10	chr8:125484400-125489000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:125484400-125489600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:125484600-125486800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr8:125484600-125487600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:125484600-125488600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr8:125484600-125488600	Active TSS	NHDF-Ad	bronchial
16	chr8:125484600-125489200	Active TSS	Right Ventricle	heart
17	chr8:125484800-125486800	Active TSS	Right Atrium	heart
18	chr8:125484800-125488400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr8:125484800-125488400	Active TSS	HSMMtube	muscle
20	chr8:125484800-125488400	Active TSS	NH-A	brain
21	chr8:125484800-125489000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:125484800-125489200	Active TSS	Aorta	Aorta
23	chr8:125484800-125489200	Active TSS	Ovary	ovary
24	chr8:125484800-125489200	Active TSS	A549	lung
25	chr8:125484800-125489400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr8:125484800-125489400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr8:125484800-125489400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr8:125484800-125490200	Active TSS	GM12878-XiMat	blood
29	chr8:125485000-125487800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr8:125485000-125487800	Active TSS	Hela-S3	cervix
31	chr8:125485000-125488200	Active TSS	Fetal Kidney	kidney
32	chr8:125485000-125488800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr8:125485000-125488800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:125485000-125488800	Active TSS	Fetal Intestine Large	intestine
35	chr8:125485000-125488800	Active TSS	Fetal Intestine Small	intestine
36	chr8:125485000-125488800	Active TSS	HMEC	breast
37	chr8:125485000-125488800	Active TSS	NHEK	skin
38	chr8:125485200-125486400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr8:125485200-125486400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr8:125485200-125486400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr8:125485200-125486600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr8:125485200-125488400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr8:125485200-125488600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:125485200-125488600	Active TSS	Placenta	Placenta
45	chr8:125485200-125489000	Active TSS	Fetal Muscle Trunk	muscle
46	chr8:125485200-125489200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr8:125485400-125486400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr8:125485400-125486800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr8:125485400-125486800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:125485400-125488000	Active TSS	Fetal Muscle Leg	muscle

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