Variant report

Variant	rs531500040
Chromosome Location	chr12:49662850-49662851
allele	A/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	chr12:49662113-49664599	U87	brain:	n/a	n/a
2	MAFK	chr12:49662305-49662870	IMR90	lung:	n/a	chr12:49662503-49662514 chr12:49662494-49662514
3	GATA3	chr12:49662488-49662978	MCF-7	breast:	n/a	n/a
4	GATA3	chr12:49662283-49663164	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:49662148-49662887	U87	brain:	n/a	n/a
6	POLR2A	chr12:49662286-49666070	K562	blood:	n/a	n/a
7	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
8	GATA3	chr12:49662186-49663076	A549	lung:	n/a	n/a
9	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
11	CEBPB	chr12:49662384-49662920	MCF-7	breast:	n/a	n/a
12	POLR2A	chr12:49662497-49662899	HepG2	liver:	n/a	n/a
13	FOSL2	chr12:49662185-49662926	A549	lung:	n/a	chr12:49662512-49662524 chr12:49662520-49662527 chr12:49662519-49662527
14	GATA3	chr12:49662585-49662862	MCF-7	breast:	n/a	n/a
15	GATA3	chr12:49662612-49662955	T-47D	breast:	n/a	n/a
16	POLR2A	chr12:49662170-49662853	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr12:49662421-49662926	HepG2	liver:	n/a	n/a
18	PBX3	chr12:49662276-49662971	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr12:49662180-49662864	HUVEC	blood vessel:	n/a	n/a
20	FOS	chr12:49662316-49663348	MCF10A-Er-Src	breast:	n/a	chr12:49662512-49662524 chr12:49662520-49662527 chr12:49662519-49662527
21	CEBPB	chr12:49662392-49662939	MCF-7	breast:	n/a	n/a
22	FOS	chr12:49662331-49663310	MCF10A-Er-Src	breast:	n/a	chr12:49662512-49662524 chr12:49662520-49662527 chr12:49662519-49662527
23	POLR2A	chr12:49662252-49662933	GM12878	blood:	n/a	n/a
24	CEBPB	chr12:49662279-49662950	A549	lung:	n/a	n/a
25	HEY1	chr12:49662207-49664643	K562	blood:	n/a	n/a
26	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr12:49662224-49662887	U87	brain:	n/a	n/a
28	EP300	chr12:49662247-49662997	SK-N-SH	brain:	n/a	chr12:49662518-49662527
29	BCLAF1	chr12:49662287-49662967	K562	blood:	n/a	chr12:49662519-49662528 chr12:49662518-49662527
30	MAX	chr12:49662214-49662928	A549	lung:	n/a	chr12:49662518-49662527 chr12:49662519-49662528
31	JUND	chr12:49662280-49662921	SK-N-SH	brain:	n/a	chr12:49662645-49662656 chr12:49662512-49662524 chr12:49662520-49662527 chr12:49662519-49662527
32	POLR2A	chr12:49662129-49664643	K562	blood:	n/a	n/a
33	POLR2A	chr12:49662291-49662943	HCT-116	colon:	n/a	n/a
34	FOS	chr12:49662331-49663375	MCF10A-Er-Src	breast:	n/a	chr12:49662512-49662524 chr12:49662520-49662527 chr12:49662519-49662527
35	POLR2A	chr12:49662412-49662913	Hela-S3	cervix:	n/a	n/a
36	GATA2	chr12:49662723-49662934	SH-SY5Y	brain:	n/a	n/a
37	POLR2A	chr12:49662157-49663034	HUVEC	blood vessel:	n/a	n/a
38	GATA3	chr12:49662214-49663142	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr12:49662713-49662958	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:49662267-49664610	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr12:49662825-49663508	HepG2	liver:	n/a	n/a
42	GATA2	chr12:49662248-49663220	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr12:49662089-49662938	K562	blood:	n/a	n/a
44	POLR2A	chr12:49662218-49666261	K562	blood:	n/a	n/a
45	POLR2A	chr12:49662250-49662984	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:49662320-49666054	A549	lung:	n/a	n/a
47	GATA3	chr12:49662702-49662858	SH-SY5Y	brain:	n/a	n/a
48	CHD1	chr12:49662080-49663241	IMR90	lung:	n/a	n/a
49	EP300	chr12:49662421-49662851	Hela-S3	cervix:	n/a	chr12:49662518-49662527
50	GATA3	chr12:49662720-49663001	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
2	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
3	chr12:49533073..49535795-chr12:49661700..49663392,2	K562	blood:
4	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
5	chr12:49661105..49664061-chr17:56709024..56710621,2	MCF-7	breast:
6	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
7	chr12:49660927..49665723-chr12:49685096..49688729,4	MCF-7	breast:
8	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
9	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
10	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
11	chr12:49500184..49504763-chr12:49658087..49663330,8	K562	blood:

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000258101	TF binding region
ENSG00000135406	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv976611	chr12:49662416-49664269	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659000-49663200	Transcr. at gene 5' and 3'	A549	lung
2	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
3	chr12:49659400-49664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49659600-49663200	Weak transcription	Fetal Brain Female	brain
5	chr12:49659600-49663400	Weak transcription	Ovary	ovary
6	chr12:49659600-49663800	Weak transcription	Brain Germinal Matrix	brain
7	chr12:49659600-49664800	Weak transcription	Fetal Lung	lung
8	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:49659800-49663000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:49659800-49663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:49659800-49663600	Weak transcription	Primary B cells from cord blood	blood
14	chr12:49659800-49663600	Weak transcription	Aorta	Aorta
15	chr12:49659800-49663600	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:49659800-49663800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:49659800-49668600	Weak transcription	Right Atrium	heart
18	chr12:49660000-49663000	Enhancers	Adipose Nuclei	Adipose
19	chr12:49660000-49663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:49660200-49663200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr12:49660200-49664000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:49660400-49663000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr12:49660400-49663200	Transcr. at gene 5' and 3'	NHEK	skin
24	chr12:49660400-49663600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:49660600-49663000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr12:49660600-49663400	Transcr. at gene 5' and 3'	Hela-S3	cervix
27	chr12:49660600-49663600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:49661000-49663000	Enhancers	Fetal Intestine Large	intestine
29	chr12:49661000-49663000	Genic enhancers	Fetal Intestine Small	intestine
30	chr12:49661000-49663000	Enhancers	Placenta	Placenta
31	chr12:49661000-49663400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:49661000-49663400	Weak transcription	Spleen	Spleen
33	chr12:49661000-49663600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:49661000-49663600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:49661000-49663600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:49661000-49663800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:49661000-49668000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr12:49661000-49669800	Strong transcription	Fetal Stomach	stomach
39	chr12:49661200-49663000	Weak transcription	Thymus	Thymus
40	chr12:49661200-49664000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:49661400-49663200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:49661400-49663400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:49661400-49663400	Weak transcription	Gastric	stomach
44	chr12:49661400-49663600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:49661600-49663000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr12:49661600-49663200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:49661600-49663200	Weak transcription	Colonic Mucosa	Colon
48	chr12:49661600-49663200	Weak transcription	Pancreas	Pancrea
49	chr12:49661600-49663200	Weak transcription	Right Ventricle	heart
50	chr12:49661600-49663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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