Variant report

Variant	rs13138554
Chromosome Location	chr4:15471069-15471070
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	MXI1	chr4:15470863-15472267	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:15471066-15471794	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
CC2D2A	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1024758	0.90[ASN][1000 genomes]
rs1024759	0.90[ASN][1000 genomes]
rs10461112	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10488970	0.88[ASN][1000 genomes]
rs12233742	0.88[ASN][1000 genomes]
rs13104095	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13114788	0.88[ASN][1000 genomes]
rs13120744	0.88[ASN][1000 genomes]
rs13123050	0.99[ASN][1000 genomes]
rs13123785	0.91[ASN][1000 genomes]
rs13124984	0.88[ASN][1000 genomes]
rs13129124	0.91[ASN][1000 genomes]
rs13132007	0.88[ASN][1000 genomes]
rs13132446	0.87[ASN][1000 genomes]
rs13132604	0.88[ASN][1000 genomes]
rs13138481	0.88[ASN][1000 genomes]
rs16891929	0.88[ASN][1000 genomes]
rs16891934	0.88[ASN][1000 genomes]
rs16891939	0.90[ASN][1000 genomes]
rs16891945	0.90[ASN][1000 genomes]
rs17469724	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1990524	0.88[ASN][1000 genomes]
rs2192355	0.88[ASN][1000 genomes]
rs2192363	0.84[EUR][1000 genomes]
rs2215810	0.84[EUR][1000 genomes]
rs28561808	0.93[ASN][1000 genomes]
rs34028526	0.88[ASN][1000 genomes]
rs34351987	0.88[ASN][1000 genomes]
rs34352292	0.88[ASN][1000 genomes]
rs34400909	0.91[ASN][1000 genomes]
rs34496443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35301498	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35465107	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35539860	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35866305	0.88[ASN][1000 genomes]
rs35971217	0.88[ASN][1000 genomes]
rs3797006	0.90[ASN][1000 genomes]
rs4140932	0.84[EUR][1000 genomes]
rs58479200	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59684117	0.88[ASN][1000 genomes]
rs61240629	0.88[ASN][1000 genomes]
rs62289285	0.88[ASN][1000 genomes]
rs66696244	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67391897	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68012715	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs71601473	0.88[ASN][1000 genomes]
rs71601477	0.91[ASN][1000 genomes]
rs722235	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7442554	0.88[ASN][1000 genomes]
rs973629	0.84[EUR][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15438800-15471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:15470600-15471200	Enhancers	H9 Cell Line	embryonic stem cell
3	chr4:15470600-15471200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:15470600-15471200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:15470600-15471200	Enhancers	Fetal Stomach	stomach
6	chr4:15470600-15472600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr4:15470800-15471200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr4:15470800-15471200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:15470800-15471200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:15470800-15471400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:15470800-15472000	Active TSS	Brain Angular Gyrus	brain
12	chr4:15470800-15472000	Active TSS	Brain Anterior Caudate	brain
13	chr4:15470800-15472600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:15470800-15473000	Active TSS	Stomach Smooth Muscle	stomach
15	chr4:15471000-15471200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr4:15471000-15471200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr4:15471000-15471200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:15471000-15471200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:15471000-15471200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:15471000-15471200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr4:15471000-15471200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:15471000-15471200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:15471000-15471200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr4:15471000-15471200	Enhancers	Primary T cells fromperipheralblood	blood
25	chr4:15471000-15471200	Enhancers	Primary hematopoietic stem cells	blood
26	chr4:15471000-15471200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr4:15471000-15471200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr4:15471000-15471200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:15471000-15471200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:15471000-15471200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:15471000-15471200	Flanking Active TSS	Aorta	Aorta
32	chr4:15471000-15471200	Enhancers	Liver	Liver
33	chr4:15471000-15471200	Active TSS	Brain Germinal Matrix	brain
34	chr4:15471000-15471200	Active TSS	Colonic Mucosa	Colon
35	chr4:15471000-15471200	Flanking Active TSS	Fetal Heart	heart
36	chr4:15471000-15471200	Enhancers	Fetal Intestine Large	intestine
37	chr4:15471000-15471200	Enhancers	Fetal Thymus	thymus
38	chr4:15471000-15471200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr4:15471000-15471200	Flanking Active TSS	A549	lung
40	chr4:15471000-15471200	Active TSS	HUVEC	blood vessel
41	chr4:15471000-15471200	Flanking Active TSS	NHDF-Ad	bronchial
42	chr4:15471000-15471400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:15471000-15471400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:15471000-15471400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr4:15471000-15471400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr4:15471000-15471400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr4:15471000-15471400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:15471000-15471400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr4:15471000-15471400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr4:15471000-15471400	Active TSS	Fetal Brain Female	brain

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