Variant report

Variant	rs9299820
Chromosome Location	chr10:26722622-26722623
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	ZNF143	chr10:26722618-26722625	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
APBB1IP	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11595895	0.90[EUR][1000 genomes]
rs12770943	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs12783726	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12783831	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335540	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1335551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1335552	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889686	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1889692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1889693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992261	0.96[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2992262	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2992263	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2992325	0.96[EUR][1000 genomes]
rs2992332	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992333	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2992334	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2992335	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3006802	0.85[EUR][1000 genomes]
rs3006807	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006808	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006810	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006811	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006813	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006835	0.96[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs35055608	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36120850	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4317881	0.83[EUR][1000 genomes]
rs4749125	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4749126	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59819668	0.85[EUR][1000 genomes]
rs7098710	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7901056	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9284109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299821	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945294	0.91[EUR][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	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1043832	chr10:26669040-26809400	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9299820	APBB1IP	cis	Thyroid	GTEx
rs9299820	APBB1IP	cis	lymphoblastoid	seeQTL
rs9299820	APBB1IP	cis	Artery Tibial	GTEx
rs9299820	ENKUR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26718400-26726400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:26718800-26724000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:26719800-26725000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:26720000-26722800	Enhancers	Primary B cells from cord blood	blood
5	chr10:26720000-26724800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:26720000-26725200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr10:26720400-26724400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:26720600-26723000	Enhancers	GM12878-XiMat	blood
9	chr10:26720600-26723400	Weak transcription	Fetal Thymus	thymus
10	chr10:26720600-26724600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr10:26720600-26725000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr10:26720600-26725000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:26720800-26724400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:26720800-26725200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr10:26721000-26724800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:26721000-26724800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:26721000-26726600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:26721200-26724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:26721200-26724800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:26721600-26723000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr10:26721600-26723000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr10:26721600-26723400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:26721800-26723000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr10:26722000-26722800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr10:26722200-26722800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr10:26722200-26722800	Enhancers	Osteobl	bone
27	chr10:26722200-26725800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:26722400-26723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:26722600-26726600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:26722600-26726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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