Variant report

Variant	rs2302653
Chromosome Location	chr2:37553484-37553485
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	TBP	chr2:37553439-37553889	Hela-S3	cervix:	n/a	n/a
2	HCFC1	chr2:37550716-37554093	Hela-S3	cervix:	n/a	n/a
3	NFYB	chr2:37553474-37553870	Hela-S3	cervix:	n/a	chr2:37553668-37553683
4	GABPA	chr2:37553384-37553884	SK-N-SH	brain:	n/a	n/a
5	MAX	chr2:37553439-37553973	SK-N-SH	brain:	n/a	n/a
6	STAT3	chr2:37553478-37553767	MCF10A-Er-Src	breast:	n/a	chr2:37553608-37553619 chr2:37553529-37553540
7	POLR2A	chr2:37553396-37553873	U87	brain:	n/a	n/a
8	POLR2A	chr2:37553382-37553778	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr2:37553472-37553689	A549	lung:	n/a	n/a
10	GATA3	chr2:37553360-37555034	SK-N-SH	brain:	n/a	chr2:37554961-37554970 chr2:37554275-37554292 chr2:37554279-37554300 chr2:37554286-37554297
11	STAT3	chr2:37553475-37553737	MCF10A-Er-Src	breast:	n/a	chr2:37553608-37553619 chr2:37553529-37553540
12	POLR2A	chr2:37553393-37553840	SK-N-SH	brain:	n/a	n/a
13	PRDM1	chr2:37553326-37553975	Hela-S3	cervix:	n/a	chr2:37553528-37553542 chr2:37553600-37553614 chr2:37553599-37553614 chr2:37553527-37553542 chr2:37553601-37553614
14	POLR2A	chr2:37553389-37553906	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr2:37553338-37553672	U87	brain:	n/a	n/a
16	CEBPB	chr2:37553429-37553765	IMR90	lung:	n/a	n/a
17	YY1	chr2:37553440-37553880	SK-N-SH	brain:	n/a	n/a
18	CEBPB	chr2:37553406-37553787	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:37553482-37553903	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr2:37553347-37553672	U87	brain:	n/a	n/a

Variant related genes	Relation type
PRKD3	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11124576	0.90[ASN][1000 genomes]
rs17409947	0.90[ASN][1000 genomes]
rs17481834	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2110963	0.86[ASN][1000 genomes]
rs2160394	0.86[ASN][1000 genomes]
rs2888463	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3770763	0.84[AFR][1000 genomes]
rs3819892	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4670192	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4670194	0.87[EUR][1000 genomes]
rs4670689	0.87[EUR][1000 genomes]
rs56059107	0.86[ASN][1000 genomes]
rs59262093	0.93[ASN][1000 genomes]
rs6726709	0.86[ASN][1000 genomes]
rs72792835	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs876461	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv2685	chr2:37550096-37594923	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37548800-37554000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:37549400-37554000	Active TSS	Right Atrium	heart
3	chr2:37549800-37553800	Active TSS	Duodenum Mucosa	Duodenum
4	chr2:37549800-37553800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr2:37549800-37554200	Active TSS	Stomach Smooth Muscle	stomach
6	chr2:37549800-37554200	Active TSS	NHLF	lung
7	chr2:37550000-37554400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:37550200-37553800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:37550200-37553800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:37550400-37554000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr2:37550400-37554000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:37551200-37553800	Active TSS	Brain Anterior Caudate	brain
13	chr2:37552200-37553600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:37552400-37553600	Flanking Active TSS	Hela-S3	cervix
15	chr2:37552800-37553600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:37552800-37553600	Weak transcription	Aorta	Aorta
17	chr2:37552800-37553600	Weak transcription	Ovary	ovary
18	chr2:37552800-37553800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:37552800-37553800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:37552800-37553800	Weak transcription	Stomach Mucosa	stomach
21	chr2:37552800-37554000	Active TSS	Brain Hippocampus Middle	brain
22	chr2:37552800-37554000	Enhancers	Fetal Intestine Small	intestine
23	chr2:37552800-37554000	Bivalent Enhancer	A549	lung
24	chr2:37552800-37554200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:37552800-37554400	Enhancers	Fetal Intestine Large	intestine
26	chr2:37553000-37553600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:37553000-37553600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:37553000-37553800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:37553000-37553800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:37553000-37553800	Enhancers	HUVEC	blood vessel
31	chr2:37553000-37554000	Active TSS	Osteobl	bone
32	chr2:37553000-37554200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:37553000-37554200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:37553000-37555200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:37553200-37553600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:37553200-37553600	Enhancers	Fetal Muscle Trunk	muscle
37	chr2:37553200-37553800	Active TSS	Adipose Nuclei	Adipose
38	chr2:37553200-37553800	Enhancers	HSMM	muscle
39	chr2:37553200-37553800	Active TSS	NHDF-Ad	bronchial
40	chr2:37553200-37554000	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:37553200-37554000	Enhancers	Rectal Smooth Muscle	rectum
42	chr2:37553200-37554200	Weak transcription	Placenta	Placenta
43	chr2:37553200-37555000	Weak transcription	Small Intestine	intestine
44	chr2:37553400-37553800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:37553400-37553800	Active TSS	HMEC	breast
46	chr2:37553400-37554000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:37553400-37554000	Active TSS	Liver	Liver
48	chr2:37553400-37554400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:37553400-37554400	Enhancers	Fetal Lung	lung
50	chr2:37553400-37554600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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