Variant report

Variant	rs62412556
Chromosome Location	chr6:56587245-56587246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs11961141	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11961342	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11968575	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970648	0.88[EUR][1000 genomes]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13192567	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13196211	0.81[EUR][1000 genomes]
rs13198399	0.99[EUR][1000 genomes]
rs13198938	0.99[EUR][1000 genomes]
rs13203000	0.98[EUR][1000 genomes]
rs13205013	0.83[EUR][1000 genomes]
rs13206849	0.83[EUR][1000 genomes]
rs13208409	0.80[EUR][1000 genomes]
rs13210876	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13213878	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217390	0.98[EUR][1000 genomes]
rs13219546	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs16888118	0.83[EUR][1000 genomes]
rs16888124	0.83[EUR][1000 genomes]
rs16888126	0.80[EUR][1000 genomes]
rs16888128	0.84[EUR][1000 genomes]
rs16888130	0.84[EUR][1000 genomes]
rs16888133	0.82[EUR][1000 genomes]
rs16888135	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17751682	0.83[EUR][1000 genomes]
rs17751695	0.83[EUR][1000 genomes]
rs2967960	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2967963	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002003	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002004	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002006	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002007	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002008	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002009	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002010	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002011	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34429594	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34455199	0.98[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	0.98[EUR][1000 genomes]
rs34566275	0.98[EUR][1000 genomes]
rs34576803	0.81[EUR][1000 genomes]
rs34587484	0.98[EUR][1000 genomes]
rs34623351	0.98[EUR][1000 genomes]
rs34703847	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34724718	0.83[EUR][1000 genomes]
rs34803237	0.98[EUR][1000 genomes]
rs34812826	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34824960	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34832779	0.97[EUR][1000 genomes]
rs35089136	0.81[EUR][1000 genomes]
rs35206656	0.84[EUR][1000 genomes]
rs35326806	0.97[EUR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35494794	0.97[EUR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.84[EUR][1000 genomes]
rs35876418	0.98[EUR][1000 genomes]
rs35920751	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36068365	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4072271	0.84[EUR][1000 genomes]
rs4074101	0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.80[EUR][1000 genomes]
rs41267675	0.98[EUR][1000 genomes]
rs4275049	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4640889	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs59085778	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59247267	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60498201	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412526	0.83[EUR][1000 genomes]
rs62412528	0.83[EUR][1000 genomes]
rs62412531	0.83[EUR][1000 genomes]
rs62412532	0.83[EUR][1000 genomes]
rs62412544	0.91[EUR][1000 genomes]
rs6901176	0.83[EUR][1000 genomes]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6938003	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs7767128	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
2	chr6:56579400-56592000	Weak transcription	Lung	lung
3	chr6:56580800-56592000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:56580800-56595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:56581000-56589200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56581000-56589200	Weak transcription	HSMMtube	muscle
7	chr6:56581000-56590000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:56581200-56587800	Weak transcription	Fetal Heart	heart
9	chr6:56581200-56589000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:56581200-56590200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:56581400-56588600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:56581400-56588600	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:56581400-56589200	Weak transcription	Brain Angular Gyrus	brain
14	chr6:56581400-56589200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:56581400-56592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:56581600-56588600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:56581600-56588600	Weak transcription	Psoas Muscle	Psoas
18	chr6:56581600-56588800	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:56581600-56588800	Weak transcription	NHDF-Ad	bronchial
20	chr6:56581600-56589000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:56581600-56589200	Weak transcription	NHLF	lung
22	chr6:56581600-56597800	Weak transcription	Fetal Brain Male	brain
23	chr6:56582400-56588600	Weak transcription	Brain Anterior Caudate	brain
24	chr6:56582600-56589200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:56582600-56589200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:56583000-56589200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:56583600-56591200	Weak transcription	NHEK	skin
29	chr6:56583800-56590800	Weak transcription	HMEC	breast
30	chr6:56584400-56588400	Weak transcription	Osteobl	bone
31	chr6:56584400-56588600	Weak transcription	NH-A	brain
32	chr6:56584400-56589000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:56584600-56589200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:56584600-56593600	Weak transcription	HUVEC	blood vessel
35	chr6:56584800-56599800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:56585000-56588000	Weak transcription	Left Ventricle	heart
37	chr6:56585200-56588800	Weak transcription	HepG2	liver
38	chr6:56586000-56587600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:56586000-56590000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:56586200-56589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:56586200-56590000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:56586400-56595600	Weak transcription	Adipose Nuclei	Adipose
43	chr6:56586600-56587800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr6:56586600-56588200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr6:56586600-56588600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:56586600-56588600	Strong transcription	HSMM	muscle
47	chr6:56586800-56587400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:56586800-56592000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:56586800-56593600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:56587000-56588600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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