Variant report

Variant	rs11687876
Chromosome Location	chr2:55428680-55428681
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1134722	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686766	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11686912	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12989854	0.84[EUR][1000 genomes]
rs12995548	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13000786	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003020	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13012567	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13014752	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13017468	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032294	0.81[EUR][1000 genomes]
rs2028139	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34447956	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35141050	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35183885	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35227659	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35700883	0.84[EUR][1000 genomes]
rs36121000	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4318424	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6742306	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6743339	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6747466	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71414544	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71414545	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71414546	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71414547	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71414548	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71414549	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71414556	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71414557	0.89[EUR][1000 genomes];0.86[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	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

No data

Chromatin state (count:67 , 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	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
4	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
5	chr2:55416200-55428800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
8	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55418400-55433600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:55419200-55429600	Weak transcription	Fetal Intestine Large	intestine
12	chr2:55419400-55434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:55419600-55431800	Weak transcription	Fetal Heart	heart
14	chr2:55420400-55433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:55420600-55433600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:55421000-55433600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:55421800-55432000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:55423200-55438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:55423600-55431000	Weak transcription	Gastric	stomach
20	chr2:55423800-55432800	Weak transcription	Pancreas	Pancrea
21	chr2:55423800-55448000	Weak transcription	HSMM	muscle
22	chr2:55424200-55432600	Weak transcription	HSMMtube	muscle
23	chr2:55424200-55432800	Weak transcription	NHEK	skin
24	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:55424400-55434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:55424400-55435000	Weak transcription	Osteobl	bone
27	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:55424600-55428800	Weak transcription	Dnd41	blood
29	chr2:55424600-55430200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:55424600-55430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:55424600-55430800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:55424600-55431200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
35	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
37	chr2:55424600-55451200	Weak transcription	HepG2	liver
38	chr2:55424800-55434000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:55425000-55430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:55425200-55429200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:55427000-55428800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:55427000-55430000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:55427000-55432200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:55427200-55430000	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:55427400-55429200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:55427400-55429200	Weak transcription	Left Ventricle	heart
49	chr2:55427400-55429400	Weak transcription	Fetal Intestine Small	intestine
50	chr2:55427400-55432600	Weak transcription	Fetal Stomach	stomach

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