Variant report

Variant	rs7980541
Chromosome Location	chr12:123379477-123379478
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	YY1	chr12:123379220-123379622	K562	blood:	n/a	n/a
2	RCOR1	chr12:123379159-123379655	K562	blood:	n/a	n/a
3	POLR2A	chr12:123379431-123379529	GM12878	blood:	n/a	n/a
4	MAX	chr12:123379119-123379577	H1-hESC	embryonic stem cell:	n/a	chr12:123379480-123379491
5	RUNX3	chr12:123379143-123379712	GM12878	blood:	n/a	n/a
6	GATA1	chr12:123378222-123379845	PBDE	blood:	n/a	n/a
7	MAX	chr12:123379159-123379705	SK-N-SH	brain:	n/a	chr12:123379480-123379491
8	MAX	chr12:123379121-123379620	ECC-1	luminal epithelium:	n/a	chr12:123379480-123379491
9	MAX	chr12:123378912-123379763	K562	blood:	n/a	chr12:123379480-123379491
10	STAT3	chr12:123379386-123379499	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr12:123379361-123379761	K562	blood:	n/a	n/a
12	CHD1	chr12:123379244-123379490	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr12:123379187-123379601	K562	blood:	n/a	n/a
14	TEAD4	chr12:123379089-123379668	K562	blood:	n/a	n/a
15	JUND	chr12:123379146-123379685	K562	blood:	n/a	n/a
16	ZBTB7A	chr12:123379219-123379849	K562	blood:	n/a	n/a
17	MAX	chr12:123379120-123379604	MCF-7	breast:	n/a	chr12:123379480-123379491
18	RAD21	chr12:123379407-123379675	GM12878	blood:	n/a	n/a
19	EP300	chr12:123379158-123379712	K562	blood:	n/a	chr12:123379598-123379611
20	POLR2A	chr12:123378536-123380847	MCF10A-Er-Src	breast:	n/a	n/a
21	MAZ	chr12:123379327-123379703	K562	blood:	n/a	chr12:123379480-123379491
22	CTCF	chr12:123379380-123379530	HBMEC	blood vessel:	n/a	n/a
23	STAT5A	chr12:123379080-123379560	K562	blood:	n/a	chr12:123379163-123379175
24	MXI1	chr12:123379103-123379635	GM12878	blood:	n/a	chr12:123379480-123379489
25	MAX	chr12:123379177-123379542	Hela-S3	cervix:	n/a	chr12:123379480-123379491
26	RCOR1	chr12:123379256-123379504	K562	blood:	n/a	n/a
27	TEAD4	chr12:123378679-123379749	K562	blood:	n/a	n/a
28	MAZ	chr12:123379145-123381201	IMR90	lung:	n/a	chr12:123379480-123379491
29	RUNX3	chr12:123379087-123379539	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:123379198-123380024	K562	blood:	n/a	n/a
31	POLR2A	chr12:123378859-123380104	K562	blood:	n/a	n/a
32	STAT3	chr12:123379307-123379493	MCF10A-Er-Src	breast:	n/a	n/a
33	MAX	chr12:123379171-123379489	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr12:123379129-123379629	K562	blood:	n/a	chr12:123379480-123379491
35	HDAC2	chr12:123379174-123379575	K562	blood:	n/a	n/a
36	E2F6	chr12:123379201-123379686	K562	blood:	n/a	n/a
37	MAX	chr12:123379176-123379710	NB4	blood:	n/a	chr12:123379480-123379491
38	MAX	chr12:123378975-123379880	HCT-116	colon:	n/a	chr12:123379480-123379491
39	STAT3	chr12:123379233-123379515	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr12:123379235-123379526	GM12878	blood:	n/a	chr12:123379480-123379491
41	MYC	chr12:123379191-123379869	MCF10A-Er-Src	breast:	n/a	chr12:123379480-123379491
42	POLR2A	chr12:123379021-123379671	K562	blood:	n/a	n/a
43	POLR2A	chr12:123379094-123379733	PANC-1	pancreas:	n/a	n/a
44	EBF1	chr12:123379132-123379641	GM12878	blood:	n/a	n/a
45	CTCF	chr12:123379440-123379590	Caco-2	colon:	n/a	n/a
46	MYC	chr12:123379182-123379717	K562	blood:	n/a	chr12:123379480-123379491
47	POLR2A	chr12:123379251-123380978	Hela-S3	cervix:	n/a	n/a
48	SMC3	chr12:123379436-123379513	GM12878	blood:	n/a	n/a
49	CTCF	chr12:123379375-123379794	K562	blood:	n/a	n/a
50	TBP	chr12:123379079-123379808	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123377544..123379506-chr12:123429321..123431444,2	MCF-7	breast:
2	chr12:123378963..123380595-chr17:56707601..56709189,2	MCF-7	breast:
3	chr12:123346271..123349232-chr12:123377793..123379796,2	K562	blood:
4	chr12:123377844..123381497-chr12:123716230..123718980,3	K562	blood:
5	chr12:123355933..123357832-chr12:123377792..123379853,2	K562	blood:

Variant related genes	Relation type
VPS37B	TF binding region
ENSG00000139722	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10744422	0.98[EUR][1000 genomes]
rs10744434	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773627	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10773657	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10847826	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10847869	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12255	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12298151	0.81[ASN][1000 genomes]
rs12313006	0.81[ASN][1000 genomes]
rs12426809	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1532835	0.91[EUR][1000 genomes]
rs1587856	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2061098	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2061101	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2135014	0.91[EUR][1000 genomes]
rs2271049	0.80[ASN][1000 genomes]
rs2271051	0.83[ASN][1000 genomes]
rs2292132	0.89[EUR][1000 genomes]
rs2292134	0.91[EUR][1000 genomes]
rs2292135	0.91[EUR][1000 genomes]
rs2292136	0.86[ASN][1000 genomes]
rs2292138	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292139	0.83[ASN][1000 genomes]
rs2343108	0.90[EUR][1000 genomes]
rs2343109	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2343685	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2880678	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817094	0.89[EUR][1000 genomes]
rs3825143	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3852536	0.91[EUR][1000 genomes]
rs3852537	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759355	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759381	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4759382	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4759386	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4759387	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4759389	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59192320	0.83[ASN][1000 genomes]
rs7138398	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7139055	1.00[EUR][1000 genomes]
rs7959441	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972447	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs897385	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897386	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897391	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs897393	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs921808	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs936083	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937766	0.91[EUR][1000 genomes]

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	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' 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	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123366200-123379800	Weak transcription	Ovary	ovary
2	chr12:123371600-123380000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr12:123373800-123379600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:123377800-123379800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:123377800-123379800	Flanking Active TSS	Fetal Heart	heart
6	chr12:123378000-123379600	Flanking Active TSS	NHDF-Ad	bronchial
7	chr12:123378000-123379800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:123378000-123379800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr12:123378000-123379800	Transcr. at gene 5' and 3'	NHEK	skin
10	chr12:123378000-123380000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr12:123378000-123380000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr12:123378000-123380000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:123378000-123380000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr12:123378000-123381000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:123378200-123379600	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:123378200-123381200	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:123378400-123379600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:123378400-123379800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr12:123378400-123380000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:123378400-123380000	Flanking Active TSS	NH-A	brain
21	chr12:123378400-123380400	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr12:123378400-123381000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:123378600-123379800	Flanking Active TSS	Colonic Mucosa	Colon
24	chr12:123378600-123379800	Flanking Active TSS	Fetal Stomach	stomach
25	chr12:123378600-123379800	Flanking Active TSS	NHLF	lung
26	chr12:123378600-123380000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr12:123378600-123380000	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr12:123378600-123380000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:123378600-123380000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:123378600-123380000	Flanking Active TSS	HUVEC	blood vessel
31	chr12:123378600-123380200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:123378600-123380200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr12:123378600-123380200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr12:123378600-123380200	Flanking Active TSS	Liver	Liver
35	chr12:123378600-123380200	Flanking Active TSS	Fetal Brain Male	brain
36	chr12:123378600-123380800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:123378800-123379600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:123378800-123379600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:123378800-123379600	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:123378800-123379600	Flanking Active TSS	HSMMtube	muscle
41	chr12:123378800-123379800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:123378800-123379800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
43	chr12:123378800-123379800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr12:123378800-123379800	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr12:123378800-123379800	Flanking Active TSS	Fetal Lung	lung
46	chr12:123378800-123379800	Flanking Active TSS	Right Atrium	heart
47	chr12:123378800-123379800	Flanking Active TSS	Right Ventricle	heart
48	chr12:123378800-123380000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:123378800-123380000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr12:123378800-123380000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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