Variant report

Variant	rs12745098
Chromosome Location	chr1:154156329-154156330
allele	C/G/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	JUN	chr1:154154490-154156460	K562	blood:	n/a	chr1:154155441-154155452 chr1:154154531-154154543
2	POLR2A	chr1:154154282-154156373	GM12878	blood:	n/a	n/a
3	GABPA	chr1:154154469-154156341	MCF-7	breast:	n/a	chr1:154155404-154155411
4	NR2F2	chr1:154154492-154156349	K562	blood:	n/a	chr1:154155249-154155264
5	CHD1	chr1:154155822-154156368	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF384	chr1:154156191-154156421	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:154156294-154156546	K562	blood:	n/a	n/a
8	RFX5	chr1:154155693-154156329	H1-hESC	embryonic stem cell:	n/a	chr1:154155883-154155896 chr1:154155881-154155896 chr1:154155881-154155896 chr1:154155881-154155896 chr1:154155883-154155898 chr1:154155880-154155897
9	TAF1	chr1:154154858-154156364	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:154154342-154156493	SK-N-MC	brain:	n/a	n/a
11	NR2F2	chr1:154155060-154156336	MCF-7	breast:	n/a	chr1:154155249-154155264
12	POLR2A	chr1:154154287-154156402	PFSK-1	brain:	n/a	n/a
13	HCFC1	chr1:154154309-154156525	Hela-S3	cervix:	n/a	n/a
14	SP1	chr1:154155477-154156457	H1-hESC	embryonic stem cell:	n/a	chr1:154155952-154155959
15	SP1	chr1:154155592-154156469	H1-hESC	embryonic stem cell:	n/a	chr1:154155952-154155959
16	SIN3A	chr1:154154526-154156391	H1-hESC	embryonic stem cell:	n/a	chr1:154155423-154155432
17	MXI1	chr1:154154298-154156427	SK-N-SH	brain:	n/a	chr1:154155880-154155895 chr1:154155882-154155897
18	ZNF384	chr1:154154782-154156540	K562	blood:	n/a	n/a
19	NR2F2	chr1:154155563-154156331	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:154154273-154156477	H1-hESC	embryonic stem cell:	n/a	n/a
21	NR2F2	chr1:154154873-154156341	K562	blood:	n/a	chr1:154155249-154155264
22	E2F6	chr1:154155581-154156338	A549	lung:	n/a	chr1:154155775-154155786 chr1:154155756-154155767 chr1:154155755-154155767
23	PML	chr1:154154352-154156380	GM12878	blood:	n/a	n/a
24	MTA3	chr1:154154328-154156391	GM12878	blood:	n/a	n/a
25	REST	chr1:154154597-154156335	H1-neurons	neurons:	n/a	chr1:154155149-154155162

No.	Distal block	Cell Line	Cell type
1	chr1:154151605..154157694-chr1:154191153..154195788,18	MCF-7	breast:
2	chr1:154140357..154146704-chr1:154153646..154156969,7	MCF-7	breast:
3	chr1:154155753..154156362-chr1:173836761..173837295,2	Hela-S3	cervix:
4	chr1:154155037..154157341-chr1:154243497..154245632,3	MCF-7	breast:
5	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
6	chr1:153961881..153966027-chr1:154151379..154156773,10	MCF-7	breast:
7	chr1:154155826..154156719-chr11:67168555..67169361,2	Hela-S3	cervix:
8	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
9	chr1:154154370..154156741-chr1:154377003..154381011,5	MCF-7	breast:
10	chr1:154153643..154157449-chr1:154190048..154195510,8	K562	blood:
11	chr1:153940285..153941977-chr1:154154150..154156390,2	MCF-7	breast:
12	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
13	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
14	chr1:153961745..153965852-chr1:154153352..154156776,9	K562	blood:
15	chr1:153966341..153968649-chr1:154153580..154156511,2	K562	blood:
16	chr1:153917479..153920688-chr1:154153090..154156398,3	MCF-7	breast:
17	chr1:153962867..153965202-chr1:154154379..154156785,3	MCF-7	breast:
18	chr1:154155278..154160143-chr1:154165338..154167782,4	K562	blood:
19	chr1:154154736..154156502-chr20:45945207..45947491,2	MCF-7	breast:
20	chr1:154154241..154157353-chr1:154161640..154168172,9	MCF-7	breast:
21	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
22	chr1:153961765..153965852-chr1:154152407..154156955,8	K562	blood:
23	chr1:154154597..154158912-chr1:154243474..154246502,4	K562	blood:
24	chr1:153915763..153918216-chr1:154155038..154156841,2	MCF-7	breast:

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000177954	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000172531	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000160712	Chromatin interaction
ENSG00000228013	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000231416	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000267882	Chromatin interaction
ENSG00000143570	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11265238	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11802893	0.91[ASN][1000 genomes]
rs12028949	0.81[AMR][1000 genomes]
rs28372838	0.81[AMR][1000 genomes]
rs35761479	0.92[ASN][1000 genomes]
rs3811455	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4620534	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676022	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3453084	chr1:154156328-154161626	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3453085	chr1:154156328-154161626	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154151600-154156400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:154152400-154156600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:154152800-154156600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:154153600-154156400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:154153800-154156400	Active TSS	GM12878-XiMat	blood
6	chr1:154153800-154156600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:154153800-154156600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:154153800-154156600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:154154000-154156400	Active TSS	Brain Germinal Matrix	brain
10	chr1:154154000-154156400	Active TSS	A549	lung
11	chr1:154154000-154157400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:154154200-154156400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:154154200-154156400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:154154200-154156400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:154154200-154156400	Active TSS	K562	blood
16	chr1:154154200-154156600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:154154400-154156400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:154154400-154156400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:154154600-154156400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:154154600-154156400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:154154600-154156400	Active TSS	HSMMtube	muscle
22	chr1:154154800-154156400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:154155000-154156600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:154155400-154156600	Active TSS	HepG2	liver
25	chr1:154155600-154156400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:154155800-154156400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr1:154155800-154156400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr1:154155800-154156400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:154155800-154156400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:154155800-154156400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:154155800-154156400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:154155800-154156400	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr1:154155800-154156400	Flanking Active TSS	Fetal Thymus	thymus
34	chr1:154155800-154156400	Flanking Active TSS	Dnd41	blood
35	chr1:154155800-154156400	Flanking Active TSS	HMEC	breast
36	chr1:154155800-154156400	Flanking Active TSS	HSMM	muscle
37	chr1:154155800-154156400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:154155800-154156400	Flanking Active TSS	NH-A	brain
39	chr1:154155800-154156400	Flanking Active TSS	NHEK	skin
40	chr1:154155800-154156600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr1:154155800-154156600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:154156000-154156400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:154156000-154156400	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:154156000-154156400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:154156000-154156400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:154156000-154156400	Flanking Active TSS	Fetal Brain Female	brain
47	chr1:154156000-154156400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:154156000-154156400	Enhancers	Small Intestine	intestine
49	chr1:154156000-154156400	Flanking Active TSS	Stomach Mucosa	stomach
50	chr1:154156000-154156600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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