Variant report

Variant	rs2992333
Chromosome Location	chr10:26727454-26727455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11595895	0.89[EUR][1000 genomes]
rs12770943	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12783726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12783831	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1335540	0.92[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1335551	0.96[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1335552	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]
rs1889686	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1889692	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1889693	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2184571	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2992261	1.00[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2992262	1.00[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2992263	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2992325	0.87[EUR][1000 genomes]
rs2992332	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2992334	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2992335	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3006802	0.83[EUR][1000 genomes]
rs3006807	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006808	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006810	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006811	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006813	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006815	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3006816	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006818	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3006819	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006821	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3006835	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs35055608	0.89[EUR][1000 genomes]
rs36120850	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4317881	0.82[EUR][1000 genomes]
rs4749125	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4749126	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59819668	0.83[EUR][1000 genomes]
rs7098710	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7901056	0.89[EUR][1000 genomes]
rs9284109	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9299819	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9299820	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]
rs9299821	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs945294	0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2992333	APBB1IP	cis	multi-tissue	Pritchard
rs2992333	APBB1IP	cis	Artery Tibial	GTEx
rs2992333	APBB1IP	cis	Thyroid	GTEx
rs2992333	ENKUR	cis	parietal	SCAN
rs2992333	MSRB2	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26725600-26730400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr10:26726000-26728000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr10:26726000-26729400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr10:26726000-26730200	Active TSS	Thymus	Thymus
5	chr10:26726000-26730800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr10:26726200-26728000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:26726200-26730200	Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr10:26726400-26727600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr10:26726400-26729200	Active TSS	Duodenum Mucosa	Duodenum
10	chr10:26726400-26729200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr10:26726400-26730200	Active TSS	Fetal Thymus	thymus
12	chr10:26726600-26727600	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr10:26726600-26727600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:26726600-26727600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:26726600-26728200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr10:26726600-26728600	Active TSS	Colonic Mucosa	Colon
17	chr10:26726600-26729400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:26726800-26727600	Enhancers	Gastric	stomach
19	chr10:26726800-26727800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
20	chr10:26726800-26728200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr10:26726800-26728200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr10:26726800-26728200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr10:26726800-26728200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr10:26726800-26728200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr10:26726800-26728200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr10:26726800-26728200	Bivalent/Poised TSS	Left Ventricle	heart
27	chr10:26726800-26728200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
28	chr10:26726800-26728600	Bivalent/Poised TSS	Fetal Stomach	stomach
29	chr10:26726800-26729000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr10:26726800-26729000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr10:26726800-26729000	Active TSS	Rectal Smooth Muscle	rectum
32	chr10:26727000-26727600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr10:26727000-26727600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr10:26727000-26727600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr10:26727000-26727800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr10:26727000-26728000	Bivalent Enhancer	Fetal Brain Male	brain
37	chr10:26727000-26728200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:26727000-26728200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr10:26727000-26728200	Active TSS	Spleen	Spleen
40	chr10:26727000-26728400	Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr10:26727000-26728600	Active TSS	Osteobl	bone
42	chr10:26727000-26729000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:26727000-26729000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:26727000-26729000	Active TSS	Esophagus	oesophagus
45	chr10:26727000-26729200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr10:26727000-26729200	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr10:26727000-26729200	Active TSS	Right Atrium	heart
48	chr10:26727000-26729400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr10:26727000-26730200	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr10:26727000-26730200	Active TSS	GM12878-XiMat	blood

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