Variant report

Variant	rs11124686
Chromosome Location	chr2:39755009-39755010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11124685	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1526024	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56337010	0.89[EUR][1000 genomes]
rs6741839	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753798	0.92[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs714855	0.91[ASN][1000 genomes]
rs72803115	0.89[EUR][1000 genomes]
rs734663	0.85[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs7565507	0.82[ASN][1000 genomes]
rs7591326	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7594967	0.89[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap]

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	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11124686	FAM82A1	cis	parietal	SCAN
rs11124686	THUMPD2	cis	parietal	SCAN
rs11124686	DHX57	cis	parietal	SCAN
rs11124686	MAP4K3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39749400-39757200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:39749400-39758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:39749400-39761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:39750000-39761000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:39750800-39760200	Weak transcription	Gastric	stomach
6	chr2:39751200-39760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:39751400-39760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:39751600-39757200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:39751800-39757000	Weak transcription	HUVEC	blood vessel
10	chr2:39752000-39755200	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:39752000-39756600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:39752200-39755200	Enhancers	Primary B cells from cord blood	blood
13	chr2:39752400-39757600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:39752600-39756600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:39752600-39756600	Weak transcription	NHDF-Ad	bronchial
16	chr2:39752600-39757000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:39752600-39757000	Weak transcription	NHEK	skin
18	chr2:39752600-39757000	Weak transcription	Osteobl	bone
19	chr2:39752600-39757200	Weak transcription	Hela-S3	cervix
20	chr2:39752600-39757200	Weak transcription	NHLF	lung
21	chr2:39752600-39760400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:39752600-39760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:39752800-39757000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:39753000-39756800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:39753000-39757000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:39753000-39757000	Weak transcription	HSMM	muscle
27	chr2:39753000-39758000	Weak transcription	Placenta	Placenta
28	chr2:39753200-39757000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:39753200-39760200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:39753400-39755800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:39753400-39756000	Weak transcription	Left Ventricle	heart
32	chr2:39753400-39757200	Weak transcription	Fetal Heart	heart
33	chr2:39753400-39757400	Weak transcription	Adipose Nuclei	Adipose
34	chr2:39753400-39757400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:39753400-39757600	Weak transcription	NH-A	brain
36	chr2:39753400-39758000	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:39753400-39761000	Weak transcription	HSMMtube	muscle
38	chr2:39753400-39768400	Weak transcription	Right Ventricle	heart
39	chr2:39753400-39768600	Weak transcription	Right Atrium	heart
40	chr2:39753600-39758200	Weak transcription	Lung	lung
41	chr2:39753600-39767000	Weak transcription	Psoas Muscle	Psoas
42	chr2:39754200-39757200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:39754400-39755400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:39754400-39757600	Weak transcription	HepG2	liver
45	chr2:39755000-39757600	Weak transcription	GM12878-XiMat	blood

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