Variant report

Variant	rs13402046
Chromosome Location	chr2:179241936-179241937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178935888..178938796-chr2:179240290..179242967,2	K562	blood:
2	chr2:179170515..179172303-chr2:179239890..179242516,2	MCF-7	breast:
3	chr2:179241346..179244043-chr2:179260000..179261898,2	K562	blood:

Variant related genes	Relation type
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10167053	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10190530	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12615771	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1434090	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1434094	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1865326	0.95[AFR][1000 genomes]
rs56303928	0.99[ASN][1000 genomes]
rs6433724	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6706330	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6706354	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6710060	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6721855	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6724982	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738236	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6738243	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6738749	0.97[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6738847	0.86[EUR][1000 genomes]
rs7580795	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7581278	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7607321	0.83[AFR][1000 genomes];0.84[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	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179183800-179247800	Weak transcription	Psoas Muscle	Psoas
2	chr2:179201800-179253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:179201800-179268200	Weak transcription	HSMM	muscle
4	chr2:179202400-179248000	Weak transcription	NH-A	brain
5	chr2:179209200-179253000	Weak transcription	Esophagus	oesophagus
6	chr2:179210800-179257200	Weak transcription	Pancreas	Pancrea
7	chr2:179215200-179248800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:179217400-179248400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:179219000-179248000	Weak transcription	Left Ventricle	heart
10	chr2:179225000-179257800	Weak transcription	Lung	lung
11	chr2:179226600-179257200	Weak transcription	Gastric	stomach
12	chr2:179228800-179247200	Weak transcription	HMEC	breast
13	chr2:179232000-179243800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:179232000-179254200	Weak transcription	Hela-S3	cervix
15	chr2:179233000-179248200	Weak transcription	Fetal Brain Male	brain
16	chr2:179235600-179251600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:179237400-179252200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:179238400-179247600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:179238400-179251400	Weak transcription	Fetal Intestine Large	intestine
20	chr2:179238600-179242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:179238600-179242600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:179238600-179247800	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:179239000-179242600	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:179239600-179242200	Strong transcription	Liver	Liver
25	chr2:179239600-179242400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:179239800-179242000	Strong transcription	Brain Anterior Caudate	brain
27	chr2:179239800-179242200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:179240000-179242400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr2:179240000-179258200	Weak transcription	NHEK	skin
30	chr2:179240200-179256800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:179240400-179242200	Strong transcription	Ovary	ovary
32	chr2:179240400-179242400	Strong transcription	HSMMtube	muscle
33	chr2:179240400-179242600	Strong transcription	Fetal Brain Female	brain
34	chr2:179240400-179242600	Strong transcription	Fetal Stomach	stomach
35	chr2:179240400-179243000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:179240600-179242400	Strong transcription	Brain Angular Gyrus	brain
37	chr2:179240800-179242200	Strong transcription	Brain Germinal Matrix	brain
38	chr2:179240800-179248000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:179240800-179249200	Weak transcription	Aorta	Aorta
40	chr2:179240800-179252000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:179240800-179253800	Weak transcription	Right Ventricle	heart
42	chr2:179241000-179242400	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:179241000-179247800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:179241000-179248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:179241200-179242600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:179241800-179242400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:179241800-179242600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:179241800-179247600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:179241800-179262600	Weak transcription	Stomach Smooth Muscle	stomach

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