Variant report

Variant	rs13395354
Chromosome Location	chr2:111600519-111600520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10185010	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13396472	0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13397960	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13401811	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1554005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72832868	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv834330	chr2:111593290-111789447	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13395354	BUB1	cis	parietal	SCAN
rs13395354	SLC20A1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111562800-111604000	Weak transcription	Lung	lung
2	chr2:111593400-111601200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:111596400-111601000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:111596400-111601200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:111596400-111603400	Weak transcription	Fetal Brain Male	brain
6	chr2:111596400-111611600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:111596600-111601200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:111596800-111601000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:111596800-111601200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:111596800-111609600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:111597000-111600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:111597000-111611400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:111597200-111600800	Weak transcription	Primary T cells from cord blood	blood
14	chr2:111597200-111601000	Weak transcription	Fetal Stomach	stomach
15	chr2:111597200-111604000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:111597400-111600800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:111597600-111601000	Weak transcription	Fetal Lung	lung
18	chr2:111597600-111604000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:111598600-111604000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:111599000-111606800	Enhancers	Fetal Thymus	thymus
21	chr2:111599400-111600800	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:111599400-111600800	Enhancers	HMEC	breast
23	chr2:111599600-111600800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:111599600-111602200	Enhancers	Dnd41	blood
25	chr2:111599800-111600800	Weak transcription	Thymus	Thymus
26	chr2:111599800-111600800	Weak transcription	GM12878-XiMat	blood
27	chr2:111600200-111601800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:111600400-111600600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:111600400-111601400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:111600400-111601600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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