Variant report

Variant	rs13029336
Chromosome Location	chr2:233569935-233569936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233560777..233562416-chr2:233568775..233570422,2	K562	blood:

Variant related genes	Relation type
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10211596	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs1022330	0.87[TSI][hapmap]
rs10933406	0.83[JPT][hapmap]
rs1104764	0.83[JPT][hapmap]
rs11535	0.83[JPT][hapmap]
rs11555646	0.87[TSI][hapmap]
rs12105766	0.83[JPT][hapmap]
rs13004406	0.87[TSI][hapmap]
rs13013142	0.87[TSI][hapmap]
rs1446311	0.87[TSI][hapmap]
rs1515961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1801251	0.87[TSI][hapmap]
rs1947105	0.87[TSI][hapmap]
rs1973675	0.86[JPT][hapmap]
rs2675954	0.83[JPT][hapmap]
rs2675968	0.83[JPT][hapmap]
rs2675974	0.87[TSI][hapmap]
rs283470	0.83[JPT][hapmap]
rs283471	0.87[TSI][hapmap]
rs283472	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283473	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs283474	0.87[TSI][hapmap]
rs283475	0.87[TSI][hapmap]
rs283476	0.87[TSI][hapmap]
rs283486	0.87[TSI][hapmap]
rs35853577	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817311	0.84[TSI][hapmap]
rs4144796	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4973564	0.83[JPT][hapmap]
rs6437071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437074	0.87[TSI][hapmap]
rs6704763	0.83[JPT][hapmap]
rs6717048	0.83[JPT][hapmap]
rs6733495	0.83[JPT][hapmap]
rs6738386	0.87[TSI][hapmap]
rs6746294	0.87[TSI][hapmap]
rs6747645	0.84[MEX][hapmap];0.87[TSI][hapmap]
rs709937	0.83[JPT][hapmap]
rs737027	0.83[JPT][hapmap]
rs748002	0.83[JPT][hapmap]
rs7557607	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558609	0.87[TSI][hapmap]
rs7595118	0.80[EUR][1000 genomes]
rs7606090	0.87[TSI][hapmap]
rs778370	0.83[JPT][hapmap]
rs938569	0.83[JPT][hapmap]
rs991873	0.83[TSI][hapmap]

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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13029336	C2orf82	cis	Skin Sun Exposed Lower leg	GTEx
rs13029336	GBX2	cis	parietal	SCAN
rs13029336	C2orf82	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563200-233572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233564000-233570600	Weak transcription	Fetal Kidney	kidney
4	chr2:233564000-233570800	Weak transcription	HSMMtube	muscle
5	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:233564000-233589000	Weak transcription	NH-A	brain
7	chr2:233564200-233570000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:233564200-233570400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:233564200-233571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:233564200-233596400	Weak transcription	NHLF	lung
11	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
14	chr2:233565200-233573800	Weak transcription	NHEK	skin
15	chr2:233565200-233589800	Weak transcription	HMEC	breast
16	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
17	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
18	chr2:233565400-233580200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
20	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:233566000-233570400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:233566000-233576000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:233566000-233576000	Strong transcription	Fetal Stomach	stomach
25	chr2:233566000-233577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:233566000-233578400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:233566000-233584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:233566200-233574200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:233566200-233576000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:233566400-233572000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:233566600-233570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:233566800-233571000	Weak transcription	Ovary	ovary
33	chr2:233566800-233571000	Weak transcription	Right Ventricle	heart
34	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
35	chr2:233567200-233574200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:233567200-233574200	Strong transcription	Fetal Thymus	thymus
37	chr2:233567400-233572200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:233567400-233576800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:233567600-233572200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:233567600-233572400	Strong transcription	GM12878-XiMat	blood
41	chr2:233567600-233577800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:233567800-233571400	Strong transcription	Left Ventricle	heart
43	chr2:233567800-233573800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:233567800-233574000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:233567800-233575800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:233568000-233572600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:233568000-233573400	Strong transcription	Dnd41	blood
48	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:233568200-233571000	Strong transcription	Fetal Brain Female	brain
50	chr2:233568200-233571200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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