Variant report

Variant	rs1567583
Chromosome Location	chr12:51664341-51664342
allele	A/C
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	CTCF	chr12:51662895-51665050	SK-N-SH	brain:	n/a	chr12:51663487-51663505 chr12:51664248-51664269 chr12:51664255-51664268 chr12:51663212-51663233 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499 chr12:51664253-51664271
2	MAX	chr12:51663212-51664801	HepG2	liver:	n/a	n/a
3	EP300	chr12:51663811-51664343	T-47D	breast:	n/a	chr12:51664070-51664079 chr12:51664011-51664020 chr12:51663920-51663936
4	POLR2A	chr12:51663835-51665220	HUVEC	blood vessel:	n/a	n/a
5	NR2F2	chr12:51663218-51664405	MCF-7	breast:	n/a	n/a
6	TCF12	chr12:51663245-51664924	ECC-1	luminal epithelium:	n/a	chr12:51663493-51663500 chr12:51664606-51664613 chr12:51663955-51663962
7	SIN3AK20	chr12:51664337-51664701	A549	lung:	n/a	n/a
8	CTCF	chr12:51664224-51664345	MCF-7	breast:	n/a	chr12:51664248-51664269 chr12:51664255-51664268 chr12:51664253-51664271
9	MAX	chr12:51663737-51664354	MCF-7	breast:	n/a	n/a
10	CTCF	chr12:51663833-51664424	K562	blood:	n/a	chr12:51664248-51664269 chr12:51664255-51664268 chr12:51664253-51664271
11	POLR2A	chr12:51663444-51664712	A549	lung:	n/a	n/a
12	RAD21	chr12:51663925-51664402	SK-N-SH_RA	brain:	n/a	chr12:51664251-51664270
13	MAZ	chr12:51663380-51665099	IMR90	lung:	n/a	n/a
14	HDAC2	chr12:51663237-51664438	MCF-7	breast:	n/a	n/a
15	TBP	chr12:51664253-51664742	HepG2	liver:	n/a	n/a
16	SIN3A	chr12:51663854-51664500	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr12:51663069-51664971	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr12:51664341-51664736	HepG2	liver:	n/a	n/a
19	TAF1	chr12:51663803-51664629	K562	blood:	n/a	n/a
20	E2F6	chr12:51663205-51664411	K562	blood:	n/a	chr12:51664070-51664080 chr12:51664105-51664114 chr12:51663901-51663911
21	POLR2A	chr12:51663832-51664350	GM12878	blood:	n/a	n/a
22	CTCF	chr12:51664200-51664350	HFF	foreskin:	n/a	chr12:51664248-51664269 chr12:51664255-51664268 chr12:51664253-51664271
23	FOSL2	chr12:51664164-51665212	A549	lung:	n/a	chr12:51664212-51664221 chr12:51664913-51664923 chr12:51664913-51664923 chr12:51664862-51664873 chr12:51664913-51664923
24	MXI1	chr12:51663886-51664808	HepG2	liver:	n/a	n/a
25	MAX	chr12:51663611-51664439	K562	blood:	n/a	n/a
26	SP1	chr12:51663115-51665261	HCT-116	colon:	n/a	chr12:51664015-51664026 chr12:51664015-51664027 chr12:51664205-51664217 chr12:51664105-51664114 chr12:51664206-51664215 chr12:51664015-51664027 chr12:51664202-51664216 chr12:51664206-51664216 chr12:51664205-51664217
27	HCFC1	chr12:51663943-51664373	K562	blood:	n/a	n/a
28	SMARCC1	chr12:51664288-51665172	Hela-S3	cervix:	n/a	n/a
29	MAX	chr12:51663106-51665113	ECC-1	luminal epithelium:	n/a	n/a
30	UBTF	chr12:51663405-51664681	K562	blood:	n/a	n/a
31	CTCF	chr12:51664220-51664370	HCT-116	colon:	n/a	chr12:51664248-51664269 chr12:51664255-51664268 chr12:51664253-51664271
32	POLR2A	chr12:51663903-51665135	SK-N-SH	brain:	n/a	n/a
33	ZBTB7A	chr12:51663251-51665153	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr12:51663862-51665031	Hela-S3	cervix:	n/a	n/a
35	GATA3	chr12:51663861-51664916	MCF-7	breast:	n/a	chr12:51664862-51664871 chr12:51664879-51664889
36	POLR2A	chr12:51663831-51665027	Hela-S3	cervix:	n/a	n/a
37	MAX	chr12:51664027-51664481	NB4	blood:	n/a	n/a
38	POLR2A	chr12:51663932-51665310	U87	brain:	n/a	n/a
39	POLR2A	chr12:51663460-51665069	HepG2	liver:	n/a	n/a
40	MXI1	chr12:51663822-51665148	IMR90	lung:	n/a	n/a
41	POLR2A	chr12:51663812-51664454	K562	blood:	n/a	n/a
42	RAD21	chr12:51664309-51665039	IMR90	lung:	n/a	n/a
43	RCOR1	chr12:51663877-51665169	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr12:51663779-51665176	Hela-S3	cervix:	n/a	n/a
45	MAX	chr12:51663889-51664433	K562	blood:	n/a	n/a
46	MAX	chr12:51662585-51665505	HCT-116	colon:	n/a	n/a
47	MXI1	chr12:51664022-51665001	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr12:51663805-51664395	HCT-116	colon:	n/a	n/a
49	EBF1	chr12:51663914-51664372	GM12878	blood:	n/a	n/a
50	POLR2A	chr12:51663406-51665111	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51664068..51664576-chr8:103876150..103876665,2	Hela-S3	cervix:
2	chr12:51476120..51478171-chr12:51663790..51665919,2	MCF-7	breast:
3	chr1:210547164..210547723-chr12:51663910..51664553,2	Hela-S3	cervix:
4	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
5	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
6	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
7	chr12:51440784..51442942-chr12:51664189..51666029,2	MCF-7	breast:
8	chr12:51475968..51477695-chr12:51663580..51665438,2	MCF-7	breast:
9	chr12:51631526..51635212-chr12:51662486..51664929,4	MCF-7	breast:
10	chr12:51661897..51665217-chr12:51739188..51742261,4	MCF-7	breast:

Variant related genes	Relation type
SMAGP	TF binding region
ENSG00000155096	Chromatin interaction
ENSG00000110934	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000139610	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11832769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579227	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12580571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1567584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125583	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3405622	chr12:51662910-51665458	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1567583	LOC57228	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51661000-51665000	Active TSS	Colonic Mucosa	Colon
2	chr12:51661400-51664800	Active TSS	Esophagus	oesophagus
3	chr12:51661600-51664600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:51661800-51664400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:51662600-51664600	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr12:51662800-51664600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:51662800-51664600	Active TSS	Gastric	stomach
8	chr12:51662800-51664800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:51662800-51664800	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr12:51662800-51664800	Active TSS	Ovary	ovary
11	chr12:51662800-51665000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr12:51662800-51665000	Active TSS	Left Ventricle	heart
13	chr12:51662800-51665000	Active TSS	Right Atrium	heart
14	chr12:51662800-51665000	Active TSS	Right Ventricle	heart
15	chr12:51662800-51665000	Active TSS	Small Intestine	intestine
16	chr12:51662800-51665400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:51663000-51664400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr12:51663000-51664400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
19	chr12:51663000-51664600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:51663000-51664600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr12:51663000-51664600	Active TSS	Brain Anterior Caudate	brain
22	chr12:51663000-51664600	Active TSS	NHLF	lung
23	chr12:51663000-51664600	Active TSS	Osteobl	bone
24	chr12:51663000-51665000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:51663000-51665000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr12:51663000-51665200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr12:51663200-51664400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:51663200-51664400	Active TSS	Primary T cells from cord blood	blood
29	chr12:51663200-51664400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:51663200-51664400	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:51663200-51664400	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr12:51663200-51664400	Active TSS	HMEC	breast
33	chr12:51663200-51664400	Active TSS	HSMMtube	muscle
34	chr12:51663200-51664600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:51663200-51664600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:51663200-51664600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr12:51663200-51664800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr12:51663200-51664800	Active TSS	Brain Angular Gyrus	brain
39	chr12:51663200-51664800	Active TSS	Colon Smooth Muscle	Colon
40	chr12:51663400-51664400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:51663400-51664400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:51663400-51664400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:51663400-51664400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:51663400-51664400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:51663400-51664400	Active TSS	Duodenum Mucosa	Duodenum
46	chr12:51663400-51664400	Active TSS	Fetal Intestine Large	intestine
47	chr12:51663400-51664400	Active TSS	Fetal Intestine Small	intestine
48	chr12:51663400-51664400	Active TSS	Pancreas	Pancrea
49	chr12:51663400-51664400	Active TSS	Psoas Muscle	Psoas
50	chr12:51663400-51664400	Active TSS	Thymus	Thymus

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