Variant report

Variant	rs229961
Chromosome Location	chr5:56986716-56986717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10057570	0.93[AFR][1000 genomes]
rs10057880	0.81[AFR][1000 genomes]
rs10069403	0.83[AMR][1000 genomes]
rs10077005	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10487613	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10487614	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12520986	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13185580	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs170740	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs170741	0.93[AFR][1000 genomes]
rs183477	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1861052	0.81[AFR][1000 genomes]
rs2017201	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2041678	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2161500	0.81[AFR][1000 genomes]
rs2191445	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2191446	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2191448	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2215420	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs229960	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs229963	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs229965	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs230846	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230853	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs230860	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230861	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2408846	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408849	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2408850	0.86[AFR][1000 genomes]
rs2898028	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4235474	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4508990	0.86[AFR][1000 genomes]
rs4699910	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4700214	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6450430	0.80[EUR][1000 genomes]
rs6450431	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6866242	0.86[AFR][1000 genomes]
rs6886241	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7726732	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732108	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7737409	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs917655	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs986101	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs991727	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:56972400-56988400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:56979600-56986800	Weak transcription	K562	blood
3	chr5:56979600-56987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:56980400-56987200	Weak transcription	Ovary	ovary
5	chr5:56984000-56988000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:56984000-56988200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:56984000-56988400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:56984200-56988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:56984200-56988400	Weak transcription	HMEC	breast
10	chr5:56984200-56988400	Weak transcription	NHEK	skin
11	chr5:56984200-56988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:56984600-56988400	Weak transcription	Psoas Muscle	Psoas
13	chr5:56985600-56990400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:56986400-56987400	Enhancers	Fetal Heart	heart
15	chr5:56986600-56987400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:56986600-56987400	Enhancers	Fetal Intestine Small	intestine
17	chr5:56986600-56987600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:56986600-56989800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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