Variant report

Variant	rs6545476
Chromosome Location	chr2:55400462-55400463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55275252..55277731-chr2:55397374..55401620,4	MCF-7	breast:
2	chr2:55224254..55226682-chr2:55399758..55402693,2	K562	blood:
3	chr2:55274533..55276717-chr2:55398790..55401683,2	K562	blood:
4	chr2:55247845..55251421-chr2:55399362..55401204,3	K562	blood:
5	chr2:55256373..55258022-chr2:55400238..55403014,2	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10176839	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[AMR][1000 genomes];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[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[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[AFR][1000 genomes];0.87[AMR][1000 genomes];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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561232	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561233	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[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	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];0.84[EUR][1000 genomes]
rs2589082	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2589083	0.84[EUR][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	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]
rs3099081	1.00[YRI][hapmap]
rs4233959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545479	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[AMR][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[AMR][1000 genomes];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[AMR][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[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[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[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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754605	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:1 , 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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55404000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55395600-55400600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:55395600-55400600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:55395600-55422800	Weak transcription	Ovary	ovary
9	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
10	chr2:55395800-55400600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55395800-55400600	Weak transcription	Fetal Kidney	kidney
12	chr2:55395800-55402400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:55395800-55403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:55395800-55403000	Weak transcription	Fetal Brain Male	brain
15	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
18	chr2:55396000-55400600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:55396200-55402600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:55396200-55407400	Weak transcription	HepG2	liver
21	chr2:55396400-55400800	Weak transcription	Fetal Lung	lung
22	chr2:55396400-55402600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:55397000-55402400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:55397000-55402400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:55397000-55402400	Weak transcription	NHDF-Ad	bronchial
26	chr2:55397000-55410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:55397200-55402600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:55397200-55402600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:55397200-55450000	Weak transcription	NH-A	brain
30	chr2:55397400-55402600	Weak transcription	NHLF	lung
31	chr2:55397400-55402600	Weak transcription	Osteobl	bone
32	chr2:55397400-55402800	Weak transcription	Brain Anterior Caudate	brain
33	chr2:55397400-55402800	Weak transcription	Brain Substantia Nigra	brain
34	chr2:55397400-55403000	Weak transcription	HSMM	muscle
35	chr2:55397400-55411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
37	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
41	chr2:55400000-55401400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:55400200-55401000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr2:55400200-55401200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:55400200-55401400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr2:55400200-55401400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:55400200-55401400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:55400200-55401600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:55400200-55401800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:55400400-55400800	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:55400400-55401000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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