Variant report

Variant	rs6545479
Chromosome Location	chr2:55427470-55427471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10176839	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10183953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191785	1.00[CEU][hapmap]
rs10439479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892007	0.82[JPT][hapmap]
rs11904107	0.82[JPT][hapmap]
rs12104902	0.82[JPT][hapmap]
rs12105731	0.82[JPT][hapmap]
rs12464094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12470507	1.00[YRI][hapmap]
rs12617316	0.82[JPT][hapmap]
rs12713290	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002841	0.82[JPT][hapmap]
rs13031346	0.82[JPT][hapmap]
rs1437387	0.82[JPT][hapmap]
rs1437388	0.82[JPT][hapmap]
rs1437389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561231	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561232	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561233	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046586	1.00[YRI][hapmap]
rs17046834	0.82[JPT][hapmap]
rs17046915	1.00[CEU][hapmap]
rs2028138	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249856	0.82[JPT][hapmap]
rs2289168	0.82[JPT][hapmap]
rs2576692	0.82[JPT][hapmap]
rs2576693	0.82[JPT][hapmap]
rs2576699	0.82[JPT][hapmap]
rs2576702	0.82[JPT][hapmap]
rs2576723	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589060	0.82[JPT][hapmap]
rs2589061	0.82[JPT][hapmap]
rs2589063	0.82[JPT][hapmap]
rs2589081	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589082	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589083	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2589111	0.82[JPT][hapmap]
rs2589113	0.82[JPT][hapmap]
rs2920845	0.86[EUR][1000 genomes]
rs2920846	0.83[EUR][1000 genomes]
rs2920869	0.86[EUR][1000 genomes]
rs2966465	0.82[JPT][hapmap]
rs2968816	0.82[JPT][hapmap]
rs2968820	0.82[JPT][hapmap]
rs2972087	0.82[JPT][hapmap]
rs4233959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545482	0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs6545484	0.82[JPT][hapmap]
rs6713058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718747	0.82[JPT][hapmap]
rs6719579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726732	0.82[JPT][hapmap]
rs6733567	0.82[JPT][hapmap]
rs6746287	0.82[JPT][hapmap]
rs6746757	1.00[CEU][hapmap]
rs6746983	1.00[CEU][hapmap]
rs6747682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747974	1.00[CEU][hapmap]
rs6750501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754605	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6759310	1.00[CEU][hapmap]
rs6759957	1.00[CEU][hapmap]
rs9784090	0.82[JPT][hapmap]

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:72 , 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	chr2:55412800-55428200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
6	chr2:55416000-55428400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55416200-55428800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
10	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55418400-55433600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:55419200-55429600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:55419400-55434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:55419600-55431800	Weak transcription	Fetal Heart	heart
16	chr2:55420000-55427800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:55420400-55427800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55420400-55433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:55420600-55433600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:55421000-55433600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:55421800-55432000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:55422800-55428000	Strong transcription	Ovary	ovary
23	chr2:55423200-55438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:55423600-55431000	Weak transcription	Gastric	stomach
25	chr2:55423800-55432800	Weak transcription	Pancreas	Pancrea
26	chr2:55423800-55448000	Weak transcription	HSMM	muscle
27	chr2:55424200-55428000	Weak transcription	Esophagus	oesophagus
28	chr2:55424200-55428400	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:55424200-55432600	Weak transcription	HSMMtube	muscle
30	chr2:55424200-55432800	Weak transcription	NHEK	skin
31	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:55424400-55434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:55424400-55435000	Weak transcription	Osteobl	bone
34	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:55424600-55427600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:55424600-55428800	Weak transcription	Dnd41	blood
37	chr2:55424600-55430200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:55424600-55430200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:55424600-55430800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:55424600-55431200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
43	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
45	chr2:55424600-55451200	Weak transcription	HepG2	liver
46	chr2:55424800-55434000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:55425000-55430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:55425200-55429200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle

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