Variant report

Variant	rs41317879
Chromosome Location	chr12:48398274-48398275
allele	A/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	POLR2A	chr12:48398011-48398504	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr12:48397501-48399134	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr12:48398173-48398812	HepG2	liver:	n/a	n/a
4	EGR1	chr12:48398087-48398620	ECC-1	luminal epithelium:	n/a	chr12:48398334-48398347 chr12:48398372-48398385
5	ZBTB7A	chr12:48397887-48399036	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:48398073-48398471	HepG2	liver:	n/a	n/a
7	TCF12	chr12:48398082-48398909	ECC-1	luminal epithelium:	n/a	chr12:48398407-48398414
8	TAF1	chr12:48398043-48398970	ECC-1	luminal epithelium:	n/a	n/a
9	GTF2F1	chr12:48398223-48398311	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr12:48397330-48399218	H1-hESC	embryonic stem cell:	n/a	chr12:48397945-48397958
11	TCF12	chr12:48397839-48399260	ECC-1	luminal epithelium:	n/a	chr12:48398407-48398414
12	MAX	chr12:48397524-48398790	ECC-1	luminal epithelium:	n/a	n/a
13	E2F6	chr12:48397408-48399034	H1-hESC	embryonic stem cell:	n/a	chr12:48398447-48398459 chr12:48398371-48398380
14	ZBTB7A	chr12:48397763-48399149	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr12:48398043-48398310	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr12:48397988-48398664	ECC-1	luminal epithelium:	n/a	n/a
17	ZNF143	chr12:48398204-48398324	H1-hESC	embryonic stem cell:	n/a	n/a
18	EP300	chr12:48397871-48398723	ECC-1	luminal epithelium:	n/a	chr12:48398369-48398385 chr12:48398373-48398389
19	YY1	chr12:48397826-48398283	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr12:48397867-48398715	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr12:48397897-48398793	ECC-1	luminal epithelium:	n/a	chr12:48398369-48398385 chr12:48398373-48398389
22	TBP	chr12:48397641-48399143	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:48397599-48398351	H1-neurons	neurons:	n/a	n/a
24	EGR1	chr12:48398078-48398712	ECC-1	luminal epithelium:	n/a	chr12:48398607-48398622 chr12:48398334-48398347 chr12:48398372-48398385
25	E2F6	chr12:48397303-48398828	H1-hESC	embryonic stem cell:	n/a	chr12:48398447-48398459 chr12:48398371-48398380
26	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
27	GABPA	chr12:48397855-48398337	H1-hESC	embryonic stem cell:	n/a	chr12:48397948-48397957
28	NFIC	chr12:48398096-48398731	ECC-1	luminal epithelium:	n/a	n/a
29	TAF1	chr12:48398123-48398466	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTBP2	chr12:48397798-48399716	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr12:48397573-48398716	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48392370..48394722-chr12:48397446..48401400,3	K562	blood:
2	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11835509	1.00[AMR][1000 genomes]
rs34093317	1.00[AMR][1000 genomes]
rs41272773	1.00[EUR][1000 genomes]
rs41317901	1.00[EUR][1000 genomes]
rs41317931	1.00[EUR][1000 genomes]
rs56932369	1.00[EUR][1000 genomes]
rs58317398	1.00[AMR][1000 genomes]
rs58559329	1.00[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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394800-48398600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
2	chr12:48394800-48398800	Bivalent Enhancer	Liver	Liver
3	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:48395000-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
5	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
6	chr12:48395200-48398600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
7	chr12:48395200-48398800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:48395400-48398600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
9	chr12:48395400-48398800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48395600-48398400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:48395600-48399000	Enhancers	Pancreas	Pancrea
12	chr12:48395800-48398400	Enhancers	Lung	lung
13	chr12:48395800-48399200	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr12:48396200-48398800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:48396400-48398400	Bivalent Enhancer	NHLF	lung
16	chr12:48396400-48398600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:48397000-48399200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:48397200-48398400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
19	chr12:48397200-48398800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:48397200-48399000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:48397200-48399200	Bivalent Enhancer	Fetal Brain Male	brain
22	chr12:48397400-48398400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
23	chr12:48397400-48398400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:48397400-48398400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
25	chr12:48397400-48398400	Flanking Bivalent TSS/Enh	A549	lung
26	chr12:48397400-48398600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr12:48397400-48398600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:48397400-48398600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr12:48397400-48398800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
30	chr12:48397400-48398800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48397400-48398800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr12:48397400-48398800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr12:48397400-48399200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr12:48397400-48399400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:48397600-48398600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:48397600-48398600	Bivalent/Poised TSS	HSMM	muscle
37	chr12:48397600-48398800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr12:48397600-48398800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr12:48397600-48398800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
40	chr12:48397600-48398800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr12:48397600-48398800	Flanking Active TSS	Right Ventricle	heart
42	chr12:48397600-48399000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
43	chr12:48397600-48399000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr12:48397600-48399400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:48397800-48398400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:48397800-48398400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:48397800-48398400	Active TSS	Aorta	Aorta
48	chr12:48397800-48398400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
49	chr12:48397800-48398600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr12:48397800-48398600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung

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