Variant report

Variant	rs2145896
Chromosome Location	chr10:116242268-116242269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11196754	0.80[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1923285	0.82[CHD][hapmap]
rs2475224	0.81[CHD][hapmap]
rs2475226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2475228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2475230	0.81[CHD][hapmap]
rs2475231	0.81[ASN][1000 genomes]
rs2497701	0.87[ASN][1000 genomes]
rs2497702	0.98[AFR][1000 genomes]
rs2497703	0.97[AFR][1000 genomes]
rs6585284	0.85[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs7067793	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7096193	0.94[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9421177	0.86[CHB][hapmap];0.87[ASN][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2145896	AP1M2	trans	parietal	SCAN
rs2145896	EMX2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116194400-116251600	Weak transcription	Small Intestine	intestine
2	chr10:116199200-116243400	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:116199600-116244600	Weak transcription	A549	lung
4	chr10:116199800-116249200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr10:116201000-116242400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:116214600-116263600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr10:116218400-116249200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:116222200-116264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:116225000-116267200	Weak transcription	Aorta	Aorta
10	chr10:116225600-116242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:116225600-116246800	Weak transcription	NHEK	skin
12	chr10:116225600-116278800	Weak transcription	HSMM	muscle
13	chr10:116227200-116247400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:116229400-116244800	Weak transcription	Thymus	Thymus
15	chr10:116230000-116243600	Weak transcription	Lung	lung
16	chr10:116231000-116244400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:116231200-116243600	Weak transcription	Fetal Thymus	thymus
18	chr10:116231200-116251600	Weak transcription	GM12878-XiMat	blood
19	chr10:116231400-116244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr10:116231800-116244800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:116231800-116249200	Weak transcription	Pancreas	Pancrea
22	chr10:116232400-116246800	Weak transcription	HMEC	breast
23	chr10:116232600-116244600	Weak transcription	Colonic Mucosa	Colon
24	chr10:116232800-116244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:116232800-116244800	Weak transcription	Hela-S3	cervix
26	chr10:116232800-116245600	Weak transcription	Brain Anterior Caudate	brain
27	chr10:116233000-116243800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:116233000-116244600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr10:116233000-116247600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:116233000-116248800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:116233200-116243400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:116233200-116245600	Weak transcription	HUVEC	blood vessel
33	chr10:116233400-116243000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr10:116233800-116244400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:116234000-116243200	Weak transcription	Fetal Intestine Small	intestine
36	chr10:116234000-116247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:116236200-116242800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:116236600-116242800	Genic enhancers	Primary T cells from cord blood	blood
39	chr10:116237200-116246200	Weak transcription	Brain Substantia Nigra	brain
40	chr10:116237400-116243000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr10:116237400-116243200	Weak transcription	Adipose Nuclei	Adipose
42	chr10:116237400-116244400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:116237400-116248800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr10:116237800-116242400	Weak transcription	Fetal Muscle Leg	muscle
45	chr10:116237800-116249000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr10:116238200-116244600	Strong transcription	Primary B cells from cord blood	blood
47	chr10:116238200-116245000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr10:116238200-116251400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr10:116238400-116242600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:116238400-116244200	Enhancers	Fetal Heart	heart

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