Variant report

Variant	rs13255599
Chromosome Location	chr8:125576963-125576964
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	chr8:125576744-125577412	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr8:125576690-125577408	HUVEC	blood vessel:	n/a	n/a
3	ZC3H11A	chr8:125576628-125577033	K562	blood:	n/a	n/a
4	POLR2A	chr8:125576878-125577017	HepG2	liver:	n/a	n/a
5	TAL1	chr8:125576787-125577153	K562	blood:	n/a	n/a
6	MAZ	chr8:125576601-125577143	K562	blood:	n/a	n/a
7	SIN3AK20	chr8:125576947-125577253	PFSK-1	brain:	n/a	n/a
8	GATA2	chr8:125576739-125577193	K562	blood:	n/a	chr8:125576970-125576977 chr8:125576970-125576977 chr8:125576965-125576981 chr8:125576967-125576981 chr8:125576968-125576978 chr8:125577159-125577169 chr8:125576970-125576977 chr8:125576963-125576984
9	POLR2A	chr8:125576877-125577186	HUVEC	blood vessel:	n/a	n/a
10	FOXP2	chr8:125576943-125577209	PFSK-1	brain:	n/a	n/a
11	ATF1	chr8:125576891-125577116	K562	blood:	n/a	n/a
12	MYC	chr8:125576908-125577169	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr8:125576898-125577202	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr8:125576874-125577176	K562	blood:	n/a	n/a
15	MAX	chr8:125576688-125577110	K562	blood:	n/a	n/a
16	CTCF	chr8:125576457-125577006	K562	blood:	n/a	chr8:125576737-125576750
17	ZMIZ1	chr8:125576650-125577161	K562	blood:	n/a	n/a
18	CEBPD	chr8:125576717-125577231	K562	blood:	n/a	n/a
19	TBL1XR1	chr8:125576844-125577245	K562	blood:	n/a	n/a
20	EP300	chr8:125576805-125577165	K562	blood:	n/a	chr8:125577034-125577043
21	ELF1	chr8:125576875-125577193	K562	blood:	n/a	chr8:125577032-125577045
22	MYC	chr8:125576582-125577227	K562	blood:	n/a	n/a
23	CUX1	chr8:125576575-125577159	K562	blood:	n/a	n/a
24	RCOR1	chr8:125576658-125577227	K562	blood:	n/a	n/a
25	GATA1	chr8:125576719-125577250	PBDE	blood:	n/a	chr8:125576970-125576977 chr8:125576970-125576977 chr8:125576965-125576981 chr8:125576968-125576978 chr8:125577159-125577169 chr8:125576970-125576977 chr8:125576963-125576984
26	TEAD4	chr8:125576671-125577268	K562	blood:	n/a	n/a
27	CCNT2	chr8:125576482-125577148	K562	blood:	n/a	n/a
28	UBTF	chr8:125576898-125576965	K562	blood:	n/a	n/a
29	GATA2	chr8:125576673-125577471	HUVEC	blood vessel:	n/a	chr8:125576970-125576977 chr8:125576970-125576977 chr8:125576965-125576981 chr8:125576967-125576981 chr8:125576968-125576978 chr8:125577159-125577169 chr8:125577263-125577273 chr8:125576970-125576977 chr8:125576963-125576984
30	JUND	chr8:125576635-125577176	K562	blood:	n/a	n/a
31	CBX3	chr8:125576389-125577323	K562	blood:	n/a	n/a
32	POLR2A	chr8:125576942-125577034	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
3	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
4	chr8:125548205..125551096-chr8:125575812..125578141,2	MCF-7	breast:
5	chr8:125575430..125576994-chr8:125827635..125829466,2	K562	blood:
6	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
7	chr8:125576007..125577952-chr8:125590257..125591907,2	MCF-7	breast:
8	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
9	chr8:125574370..125578079-chr8:125630160..125632086,3	MCF-7	breast:

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000272486	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10094916	0.93[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10099056	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10103773	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs10110655	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11778396	1.00[YRI][hapmap]
rs11783209	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12546733	0.81[AFR][1000 genomes]
rs13256399	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16899688	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs17371123	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2303955	0.90[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750232	0.88[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs3763540	0.92[ASN][1000 genomes]
rs3763541	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763542	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763543	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3763544	0.94[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs3829035	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs4489311	0.89[CEU][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6470253	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs6470254	0.90[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs6997175	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6997184	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs7010757	1.00[YRI][hapmap]
rs7015228	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7015374	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7821954	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7835397	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.92[ASN][1000 genomes]
rs7841224	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs7846270	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1024804	chr8:125575803-125600950	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
2	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
3	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:125566400-125577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:125566400-125577800	Weak transcription	Small Intestine	intestine
6	chr8:125566400-125600600	Weak transcription	NHEK	skin
7	chr8:125566600-125577200	Weak transcription	Osteobl	bone
8	chr8:125566800-125581400	Weak transcription	HSMM	muscle
9	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
10	chr8:125568200-125577000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:125570800-125605000	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:125571800-125581200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:125572000-125577000	Weak transcription	NHLF	lung
15	chr8:125574200-125577200	Enhancers	Psoas Muscle	Psoas
16	chr8:125574400-125609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr8:125574800-125580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:125574800-125581000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr8:125574800-125590200	Weak transcription	HMEC	breast
20	chr8:125575200-125577200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr8:125575200-125577400	Enhancers	Left Ventricle	heart
22	chr8:125575200-125578000	Genic enhancers	Fetal Muscle Leg	muscle
23	chr8:125575200-125578200	Enhancers	Lung	lung
24	chr8:125575200-125578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:125575400-125577200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr8:125575400-125577400	Weak transcription	Gastric	stomach
27	chr8:125575400-125589200	Weak transcription	Esophagus	oesophagus
28	chr8:125575600-125577200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:125575600-125577200	Genic enhancers	Brain Inferior Temporal Lobe	brain
30	chr8:125575600-125577400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr8:125575600-125577600	Enhancers	Duodenum Mucosa	Duodenum
32	chr8:125575600-125577600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr8:125575600-125577800	Enhancers	Adipose Nuclei	Adipose
34	chr8:125575600-125577800	Enhancers	Stomach Mucosa	stomach
35	chr8:125575600-125578400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:125575600-125600600	Weak transcription	Fetal Kidney	kidney
37	chr8:125575800-125577000	Enhancers	Spleen	Spleen
38	chr8:125575800-125577200	Weak transcription	Brain Germinal Matrix	brain
39	chr8:125575800-125577400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr8:125575800-125577400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr8:125575800-125577600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr8:125575800-125577600	Enhancers	Brain Substantia Nigra	brain
43	chr8:125575800-125577600	Flanking Active TSS	Dnd41	blood
44	chr8:125575800-125577800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr8:125575800-125578000	Enhancers	NHDF-Ad	bronchial
46	chr8:125575800-125578600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:125575800-125578600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr8:125575800-125581000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:125575800-125589200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr8:125576000-125577000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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