Variant report

Variant	rs2864818
Chromosome Location	chr2:55433976-55433977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10197309	0.80[AMR][1000 genomes]
rs1133181	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1133182	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11679663	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11685292	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12616435	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12619400	0.81[ASN][1000 genomes]
rs12621144	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012766	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13013134	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019355	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13021215	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13023235	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13417057	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs14026	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164714	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2576710	0.86[AMR][1000 genomes]
rs2576724	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34054131	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34564471	0.85[ASN][1000 genomes]
rs35026006	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35161040	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35890669	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762509	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3935223	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4420737	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671241	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671242	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672024	0.85[ASN][1000 genomes]
rs4672026	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672027	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56095114	0.97[ASN][1000 genomes]
rs56339196	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6545474	0.80[EUR][1000 genomes]
rs6545475	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6545478	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7595134	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2864818	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55419400-55434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:55423200-55438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:55423800-55448000	Weak transcription	HSMM	muscle
11	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:55424400-55434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:55424400-55435000	Weak transcription	Osteobl	bone
14	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
17	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
19	chr2:55424600-55451200	Weak transcription	HepG2	liver
20	chr2:55424800-55434000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:55427400-55434200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
26	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:55428800-55434400	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:55428800-55439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55430000-55437800	Weak transcription	Fetal Intestine Large	intestine
32	chr2:55430000-55443200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
34	chr2:55431000-55439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:55431200-55434800	Weak transcription	Brain Substantia Nigra	brain
36	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:55432000-55451200	Weak transcription	Dnd41	blood
38	chr2:55432200-55434000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:55432600-55434400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
44	chr2:55433000-55435400	Weak transcription	Primary T cells from cord blood	blood
45	chr2:55433000-55444600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
49	chr2:55433000-55450200	Weak transcription	Ovary	ovary
50	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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