Variant report

Variant	rs13401182
Chromosome Location	chr2:39932807-39932808
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	chr2:39931730..39934991-chr2:39935241..39938593,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10206408	0.88[AMR][1000 genomes]
rs11124691	0.87[AMR][1000 genomes]
rs12470473	0.83[GIH][hapmap];0.82[JPT][hapmap]
rs12623462	0.87[AMR][1000 genomes]
rs12623545	0.88[AMR][1000 genomes]
rs12624217	0.85[GIH][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs12712653	0.82[JPT][hapmap]
rs13026313	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs13425906	0.80[AMR][1000 genomes]
rs17024145	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1978327	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1986876	0.82[CHB][hapmap]
rs2058620	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2110656	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2160198	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160199	0.84[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2192686	0.85[EUR][1000 genomes]
rs2373688	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2373689	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs2540255	0.85[GIH][hapmap]
rs2716681	0.86[EUR][1000 genomes]
rs2716699	0.84[EUR][1000 genomes]
rs2716704	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2716730	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3732121	0.88[JPT][hapmap]
rs3732122	0.82[JPT][hapmap]
rs3902124	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4365444	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4644998	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670955	0.81[AMR][1000 genomes]
rs4670956	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4670957	0.82[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes]
rs4670958	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs4670959	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs6544242	0.82[JPT][hapmap]
rs6719179	0.82[CHB][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs6731450	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs6747842	0.82[JPT][hapmap]
rs6758453	0.82[JPT][hapmap]
rs7560642	0.85[GIH][hapmap];0.84[JPT][hapmap]
rs7565954	0.87[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7581406	0.88[AMR][1000 genomes]
rs917960	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs917962	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs917963	0.88[CHB][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs962262	0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes]
rs997976	0.85[GIH][hapmap];0.88[JPT][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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13401182	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39923600-39935200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
3	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
4	chr2:39931400-39934200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:39931400-39937600	Weak transcription	Brain Anterior Caudate	brain
6	chr2:39931400-39941200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:39931600-39933400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39931600-39934200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39931600-39945800	Weak transcription	Aorta	Aorta
11	chr2:39932200-39934600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:39932600-39933400	Strong transcription	HSMMtube	muscle
13	chr2:39932800-39933000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:39932800-39933000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:39932800-39933200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:39932800-39933400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:39932800-39933400	Enhancers	Fetal Thymus	thymus
18	chr2:39932800-39933400	Enhancers	NHEK	skin
19	chr2:39932800-39933600	Bivalent Enhancer	HepG2	liver
20	chr2:39932800-39933600	Enhancers	HMEC	breast
21	chr2:39932800-39934600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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