Variant report

Variant	rs4459375
Chromosome Location	chr12:48356881-48356882
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	RAD21	chr12:48356736-48358455	SK-N-SH	brain:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
2	CTCF	chr12:48356780-48356930	AG04449	skin:	n/a	n/a
3	NRF1	chr12:48356865-48357705	SK-N-SH	brain:	n/a	chr12:48357372-48357381 chr12:48357321-48357332 chr12:48357370-48357381 chr12:48357336-48357347 chr12:48357370-48357381 chr12:48357321-48357332 chr12:48357370-48357384
4	CTCF	chr12:48356824-48357775	SK-N-SH	brain:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
5	TCF12	chr12:48356881-48358078	A549	lung:	n/a	n/a
6	CTCF	chr12:48356850-48357713	HCT-116	colon:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
7	SMC3	chr12:48356860-48358490	SK-N-SH	brain:	n/a	chr12:48357572-48357582
8	CTCF	chr12:48356634-48358309	A549	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
9	CTCF	chr12:48356840-48356990	GM12865	blood:	n/a	n/a
10	RCOR1	chr12:48356453-48358490	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48298691..48299776-chr12:48356759..48358181,8	MCF-7	breast:
2	chr12:48355845..48358792-chr12:48550018..48552863,2	K562	blood:
3	chr12:48355857..48357881-chr12:48473283..48476045,2	MCF-7	breast:
4	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
5	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
6	chr12:48347971..48349706-chr12:48354609..48357059,2	MCF-7	breast:

Variant related genes	Relation type
TMEM106C	TF binding region
ENSG00000222635	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10783222	0.85[EUR][1000 genomes]
rs10783223	0.84[EUR][1000 genomes]
rs11609253	0.83[EUR][1000 genomes]
rs4073726	0.83[EUR][1000 genomes]
rs4340112	0.82[EUR][1000 genomes]
rs7970376	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48356000-48357000	Enhancers	Fetal Lung	lung
2	chr12:48356200-48357000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr12:48356400-48357000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:48356400-48357000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr12:48356400-48357000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:48356400-48357000	Enhancers	Brain Hippocampus Middle	brain
7	chr12:48356400-48357000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr12:48356600-48357000	Enhancers	Adipose Nuclei	Adipose
9	chr12:48356600-48357000	Enhancers	Brain Angular Gyrus	brain
10	chr12:48356600-48357000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr12:48356600-48357000	Enhancers	Fetal Stomach	stomach
12	chr12:48356600-48357000	Enhancers	Right Ventricle	heart
13	chr12:48356600-48357000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr12:48356600-48357000	Bivalent Enhancer	HepG2	liver
15	chr12:48356600-48357000	Enhancers	HMEC	breast
16	chr12:48356600-48357200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:48356600-48357200	Flanking Active TSS	Dnd41	blood
18	chr12:48356600-48357400	Enhancers	Fetal Heart	heart
19	chr12:48356800-48357000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:48356800-48357000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr12:48356800-48357000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:48356800-48357000	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:48356800-48357000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:48356800-48357000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:48356800-48357000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:48356800-48357000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr12:48356800-48357000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:48356800-48357000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:48356800-48357000	Bivalent Enhancer	Fetal Intestine Small	intestine
30	chr12:48356800-48357000	Enhancers	Fetal Kidney	kidney
31	chr12:48356800-48357000	Enhancers	Fetal Muscle Leg	muscle
32	chr12:48356800-48357000	Enhancers	Placenta	Placenta
33	chr12:48356800-48357000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:48356800-48357000	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:48356800-48357000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:48356800-48357000	Enhancers	K562	blood
37	chr12:48356800-48357000	Enhancers	NHEK	skin
38	chr12:48356800-48357000	Enhancers	NHLF	lung
39	chr12:48356800-48357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:48356800-48357200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr12:48356800-48357200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr12:48356800-48357200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr12:48356800-48357200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:48356800-48357200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr12:48356800-48357200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr12:48356800-48357200	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr12:48356800-48357200	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr12:48356800-48357200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:48356800-48357200	Bivalent Enhancer	Fetal Thymus	thymus
50	chr12:48356800-48357200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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