Variant report

Variant	rs1024811
Chromosome Location	chr2:37615020-37615021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165491	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10181043	0.84[ASN][1000 genomes]
rs10189370	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12475384	0.93[ASN][1000 genomes]
rs12476654	0.85[ASN][1000 genomes]
rs12987182	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13002028	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13003908	0.98[ASN][1000 genomes]
rs13014680	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13035644	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17020669	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373002	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2373106	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2373107	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34105303	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34652606	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34658454	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4490163	0.83[ASN][1000 genomes]
rs4549068	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670705	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4670713	0.83[ASN][1000 genomes]
rs6544076	0.85[ASN][1000 genomes]
rs6732454	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71437580	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430724	chr2:37546820-37628704	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1024811	QPCT	cis	lymphoblastoid	seeQTL
rs1024811	ATL2	cis	cerebellum	SCAN
rs1024811	GALM	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37604600-37616800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:37607400-37618200	Weak transcription	Right Atrium	heart
3	chr2:37609200-37615200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:37609200-37616600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:37609200-37616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:37611400-37615600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:37611800-37616800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:37612200-37616600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:37613600-37618400	Enhancers	NHDF-Ad	bronchial
10	chr2:37613800-37617200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:37614000-37617400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:37614200-37615200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:37614200-37615200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:37614200-37615600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:37614200-37615600	Enhancers	HSMM	muscle
16	chr2:37614200-37615600	Enhancers	NH-A	brain
17	chr2:37614200-37615800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:37614200-37617200	Enhancers	NHEK	skin
19	chr2:37614200-37617400	Enhancers	NHLF	lung
20	chr2:37614200-37618400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:37614200-37618600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:37614200-37618600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:37614400-37615200	Flanking Active TSS	Osteobl	bone
24	chr2:37614400-37615400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:37614400-37615600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:37614400-37615600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:37614400-37618400	Enhancers	HMEC	breast
28	chr2:37614600-37615200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:37614600-37615600	Enhancers	Esophagus	oesophagus
30	chr2:37614600-37617000	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:37614600-37617200	Enhancers	HUVEC	blood vessel
32	chr2:37614800-37615600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:37614800-37616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:37614800-37617200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:37614800-37623000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:37615000-37615200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:37615000-37615200	Enhancers	A549	lung
38	chr2:37615000-37615400	Enhancers	HSMMtube	muscle
39	chr2:37615000-37617000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:37615000-37617200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:37615000-37618800	Enhancers	Primary T helper cells PMA-I stimulated	--

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