Variant report

Variant	rs1335552
Chromosome Location	chr10:26725355-26725356
allele	C/T
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	CHD2	chr10:26725300-26725455	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
APBB1IP	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12783831	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1335540	0.87[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1335551	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1889686	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1889692	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889693	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184571	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2992261	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2992262	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2992263	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2992325	0.96[EUR][1000 genomes]
rs2992332	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2992333	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2992334	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2992335	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3006802	0.85[EUR][1000 genomes]
rs3006807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006810	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006811	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006813	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006815	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3006816	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006818	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006819	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006821	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3006835	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs35055608	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36120850	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4317881	0.83[EUR][1000 genomes]
rs4749125	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4749126	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59819668	0.85[EUR][1000 genomes]
rs7098710	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7901056	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9284109	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9299819	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9299820	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]
rs9299821	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1335552	APBB1IP	cis	Thyroid	GTEx
rs1335552	APBB1IP	cis	Artery Tibial	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26718400-26726400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:26721000-26726600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:26722200-26725800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:26722600-26726600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:26722600-26726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:26722800-26726600	Weak transcription	Osteobl	bone
7	chr10:26723000-26726000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:26723400-26726000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:26723800-26727000	Weak transcription	Spleen	Spleen
10	chr10:26724000-26726400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:26724400-26726000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr10:26724400-26726000	Enhancers	Thymus	Thymus
13	chr10:26724400-26726200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr10:26724400-26726400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr10:26724400-26726400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr10:26724400-26726400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr10:26724400-26726400	Enhancers	Liver	Liver
18	chr10:26724400-26726600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:26724600-26725600	Enhancers	Primary B cells from cord blood	blood
20	chr10:26724600-26726400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr10:26724600-26726600	Enhancers	Primary B cells from peripheral blood	blood
22	chr10:26724800-26726000	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:26724800-26726000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr10:26724800-26726000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:26724800-26726000	Enhancers	Fetal Thymus	thymus
26	chr10:26724800-26726000	Enhancers	Dnd41	blood
27	chr10:26724800-26726200	Enhancers	Primary T cells from cord blood	blood
28	chr10:26724800-26726200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:26724800-26726400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr10:26724800-26726600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr10:26725000-26725600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:26725000-26726400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr10:26725000-26726400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:26725200-26726000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr10:26725200-26726000	Enhancers	GM12878-XiMat	blood
36	chr10:26725200-26726400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr10:26725200-26727000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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