Variant report

Variant	rs28365863
Chromosome Location	chr12:57623519-57623520
allele	A/G
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	REST	chr12:57623424-57624137	PFSK-1	brain:	n/a	n/a
2	CTCF	chr12:57623310-57623568	Spleen_OC	spleen:	n/a	n/a
3	POLR2A	chr12:57623361-57624069	HEK293	kidney:	n/a	n/a
4	ELK1	chr12:57623311-57624112	Hela-S3	cervix:	n/a	n/a
5	TFAP2A	chr12:57622778-57624185	Hela-S3	cervix:	n/a	chr12:57623801-57623815 chr12:57623310-57623321 chr12:57623310-57623321 chr12:57623310-57623321 chr12:57623309-57623323 chr12:57623311-57623326 chr12:57623309-57623323 chr12:57623310-57623321 chr12:57623330-57623345
6	ZNF384	chr12:57623210-57623572	K562	blood:	n/a	n/a
7	EBF1	chr12:57623142-57623662	GM12878	blood:	n/a	n/a
8	SIX5	chr12:57623157-57623607	H1-hESC	embryonic stem cell:	n/a	chr12:57623381-57623395 chr12:57623383-57623392 chr12:57623385-57623394
9	BHLHE40	chr12:57623336-57623986	GM12878	blood:	n/a	n/a
10	CHD2	chr12:57623404-57623601	K562	blood:	n/a	n/a
11	MAX	chr12:57623351-57624082	MCF-7	breast:	n/a	chr12:57623696-57623703
12	MAX	chr12:57623301-57624319	H1-hESC	embryonic stem cell:	n/a	chr12:57623696-57623703
13	POLR2A	chr12:57622967-57627887	H1-hESC	embryonic stem cell:	n/a	n/a
14	ELF1	chr12:57623317-57623678	HepG2	liver:	n/a	n/a
15	MAX	chr12:57623377-57624074	HepG2	liver:	n/a	chr12:57623696-57623703
16	POLR2A	chr12:57623345-57624422	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:57622661-57625191	U87	brain:	n/a	n/a
18	POLR2A	chr12:57622952-57624837	GM12892	blood:	n/a	n/a
19	POU2F2	chr12:57623319-57624041	GM12878	blood:	n/a	n/a
20	ZNF143	chr12:57623155-57623920	GM12878	blood:	n/a	chr12:57623383-57623401 chr12:57623383-57623392 chr12:57623385-57623394
21	POLR2A	chr12:57623248-57624437	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr12:57623406-57624075	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:57622811-57628074	HepG2	liver:	n/a	n/a
24	CEBPB	chr12:57623258-57623852	GM12878	blood:	n/a	n/a
25	TBP	chr12:57623321-57624328	H1-hESC	embryonic stem cell:	n/a	n/a
26	EBF1	chr12:57623233-57623524	GM12878	blood:	n/a	n/a
27	MXI1	chr12:57622692-57624810	IMR90	lung:	n/a	chr12:57623211-57623226
28	MYC	chr12:57623377-57624185	HUVEC	blood vessel:	n/a	chr12:57623696-57623703
29	ZNF143	chr12:57623194-57623637	H1-hESC	embryonic stem cell:	n/a	chr12:57623383-57623401 chr12:57623383-57623392 chr12:57623385-57623394
30	POLR2A	chr12:57623360-57624827	GM12878	blood:	n/a	n/a
31	YY1	chr12:57623307-57624089	HepG2	liver:	n/a	n/a
32	MAX	chr12:57623338-57624141	SK-N-SH	brain:	n/a	chr12:57623696-57623703
33	MYBL2	chr12:57623213-57623715	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:57622648-57625404	PFSK-1	brain:	n/a	n/a
35	TAF1	chr12:57623286-57623990	Hela-S3	cervix:	n/a	n/a
36	ETS1	chr12:57623097-57624059	A549	lung:	n/a	chr12:57623381-57623394 chr12:57623382-57623395
37	RFX5	chr12:57623420-57623624	K562	blood:	n/a	n/a
38	SMC3	chr12:57623346-57624075	Hela-S3	cervix:	n/a	n/a
39	MYC	chr12:57623294-57624144	Hela-S3	cervix:	n/a	chr12:57623696-57623703
40	POLR2A	chr12:57623325-57624633	GM15510	blood:	n/a	n/a
41	NRF1	chr12:57623219-57623665	H1-hESC	embryonic stem cell:	n/a	chr12:57623416-57623430 chr12:57623419-57623430 chr12:57623471-57623480 chr12:57623419-57623433 chr12:57623470-57623481 chr12:57623471-57623482
42	TAF1	chr12:57623162-57624569	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr12:57623286-57624200	HL-60	blood:	n/a	n/a
44	CHD2	chr12:57623437-57624135	HepG2	liver:	n/a	n/a
45	CTCF	chr12:57623393-57623536	Kidney_OC	kidney:	n/a	n/a
46	MAZ	chr12:57623133-57623676	HepG2	liver:	n/a	n/a
47	ZC3H11A	chr12:57623478-57623547	K562	blood:	n/a	n/a
48	POLR2A	chr12:57623368-57623627	A549	lung:	n/a	n/a
49	CTCF	chr12:57623380-57623530	HMF	breast:	n/a	n/a
50	POLR2A	chr12:57623341-57624276	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57480170..57482164-chr12:57622267..57624511,2	MCF-7	breast:
2	chr12:54673520..54675389-chr12:57621461..57623953,2	MCF-7	breast:
3	chr12:57623383..57624007-chr19:54372006..54372555,2	NB4	blood:
4	chr12:57480219..57483297-chr12:57622863..57624907,4	MCF-7	breast:
5	chr12:57623321..57623894-chr15:65588155..65589090,2	NB4	blood:
6	chr12:57622307..57625065-chr12:57914079..57916302,2	K562	blood:

Variant related genes	Relation type
SHMT2	TF binding region
ENSG00000094916	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000228323	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11172219	1.00[EUR][1000 genomes]
rs11557166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17854829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248177	1.00[EUR][1000 genomes]
rs34950222	1.00[EUR][1000 genomes]
rs35021926	1.00[EUR][1000 genomes]
rs56273568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61978619	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62620661	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304504	1.00[EUR][1000 genomes]
rs74093103	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74093104	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74093113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74093115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74093117	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 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	chr12:57622600-57624800	Active TSS	HSMMtube	muscle
2	chr12:57622800-57623800	Active TSS	Brain Anterior Caudate	brain
3	chr12:57622800-57624400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr12:57622800-57624600	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr12:57622800-57624800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr12:57622800-57625000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:57623000-57623600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:57623000-57623600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:57623000-57624000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:57623000-57624200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr12:57623000-57624200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr12:57623000-57624200	Active TSS	Rectal Smooth Muscle	rectum
13	chr12:57623000-57624400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:57623000-57624400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:57623000-57624400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:57623000-57624400	Active TSS	A549	lung
17	chr12:57623000-57624600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr12:57623000-57624600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr12:57623000-57624600	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:57623000-57624600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr12:57623000-57624800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr12:57623000-57624800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:57623000-57624800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:57623000-57624800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr12:57623000-57624800	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr12:57623000-57624800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:57623200-57623600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:57623200-57623600	Active TSS	Fetal Muscle Trunk	muscle
29	chr12:57623200-57623600	Active TSS	Right Ventricle	heart
30	chr12:57623200-57623600	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:57623200-57623800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:57623200-57623800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:57623200-57623800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:57623200-57623800	Active TSS	Left Ventricle	heart
35	chr12:57623200-57623800	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr12:57623200-57624000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr12:57623200-57624000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:57623200-57624000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:57623200-57624000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:57623200-57624000	Active TSS	Right Atrium	heart
41	chr12:57623200-57624200	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr12:57623200-57624200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:57623200-57624200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:57623200-57624200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:57623200-57624200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr12:57623200-57624200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:57623200-57624200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr12:57623200-57624200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr12:57623200-57624200	Active TSS	Psoas Muscle	Psoas
50	chr12:57623200-57624200	Active TSS	Hela-S3	cervix

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