Variant report

Variant	rs17013336
Chromosome Location	chr3:23523334-23523335
allele	A/G
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	EP300	chr3:23523006-23523374	SK-N-SH_RA	brain:	n/a	n/a
2	PBX3	chr3:23523038-23523531	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr3:23522912-23523669	SK-N-SH	brain:	n/a	n/a
4	EP300	chr3:23522976-23523472	SK-N-SH_RA	brain:	n/a	chr3:23523373-23523383
5	TCF7L2	chr3:23522838-23524257	HEK293	kidney:	n/a	chr3:23523137-23523144
6	KAP1	chr3:23522934-23524002	U2OS	brain:	n/a	n/a
7	POLR2A	chr3:23523140-23523715	H1-neurons	neurons:	n/a	n/a
8	SETDB1	chr3:23523127-23523599	U2OS	brain:	n/a	n/a
9	GATA3	chr3:23522985-23523615	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr3:23522870-23523584	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr3:23522997-23523574	SK-N-SH	brain:	n/a	n/a
12	KAP1	chr3:23522851-23523935	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
ENSG00000265645	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7624969	1.00[AMR][1000 genomes];1.00[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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23512000-23527400	Weak transcription	Left Ventricle	heart
2	chr3:23513800-23527400	Weak transcription	Right Atrium	heart
3	chr3:23521000-23527600	Weak transcription	Right Ventricle	heart
4	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
5	chr3:23521200-23527600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:23521400-23523400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:23521600-23523400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:23521600-23527400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:23521800-23523600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:23521800-23524000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:23521800-23527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:23521800-23527600	Weak transcription	Spleen	Spleen
14	chr3:23521800-23528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:23522000-23525800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:23522000-23527400	Weak transcription	Thymus	Thymus
17	chr3:23522000-23527400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:23522000-23527800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:23522000-23531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:23522200-23523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:23522200-23527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:23522200-23527400	Weak transcription	Primary B cells from cord blood	blood
24	chr3:23522200-23527600	Weak transcription	Fetal Thymus	thymus
25	chr3:23522200-23527800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:23522200-23528000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:23522400-23523600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:23522400-23524000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:23522600-23523400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:23522600-23523400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:23522600-23523600	Enhancers	Brain Substantia Nigra	brain
32	chr3:23522600-23523600	Enhancers	Fetal Brain Male	brain
33	chr3:23522600-23523600	Enhancers	Fetal Kidney	kidney
34	chr3:23522600-23523600	Enhancers	GM12878-XiMat	blood
35	chr3:23522600-23523800	Enhancers	Fetal Lung	lung
36	chr3:23522600-23524000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:23522600-23524000	Enhancers	Brain Hippocampus Middle	brain
38	chr3:23522600-23524000	Enhancers	Fetal Muscle Leg	muscle
39	chr3:23522800-23523400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:23522800-23523400	Enhancers	Colon Smooth Muscle	Colon
41	chr3:23522800-23523600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:23522800-23524200	Enhancers	Fetal Heart	heart
43	chr3:23522800-23524200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:23523000-23523400	Enhancers	Brain Angular Gyrus	brain
45	chr3:23523000-23523400	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr3:23523000-23523600	Enhancers	Brain Anterior Caudate	brain
47	chr3:23523000-23523800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:23523000-23524200	Enhancers	HSMMtube	muscle
49	chr3:23523000-23524800	Enhancers	Psoas Muscle	Psoas
50	chr3:23523000-23530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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