Variant report

Variant	rs6659368
Chromosome Location	chr1:180629437-180629438
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10914061	0.89[ASN][1000 genomes]
rs10914096	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12085097	0.86[EUR][1000 genomes]
rs1339768	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1970404	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2331626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2331886	0.94[EUR][1000 genomes]
rs2944259	0.88[EUR][1000 genomes]
rs2944262	0.88[EUR][1000 genomes]
rs3002113	0.88[EUR][1000 genomes]
rs3002114	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002115	0.88[EUR][1000 genomes]
rs3002116	0.88[EUR][1000 genomes]
rs3002117	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002123	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3013633	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3013634	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3789366	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3843278	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845406	0.81[EUR][1000 genomes]
rs3856058	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3897798	0.86[ASN][1000 genomes]
rs4083591	0.81[EUR][1000 genomes]
rs4108558	0.95[EUR][1000 genomes]
rs66520411	0.88[EUR][1000 genomes]
rs67780680	0.93[EUR][1000 genomes]
rs72707408	0.84[EUR][1000 genomes]
rs72723045	0.88[EUR][1000 genomes]
rs7514404	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7524547	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541650	0.86[ASN][1000 genomes]
rs7548318	0.88[EUR][1000 genomes]
rs7550031	0.87[EUR][1000 genomes]
rs9425881	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180645200	Weak transcription	Gastric	stomach
2	chr1:180613200-180632600	Weak transcription	Aorta	Aorta
3	chr1:180619600-180632600	Weak transcription	Pancreas	Pancrea
4	chr1:180619600-180634600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:180625800-180634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:180627600-180632800	Weak transcription	A549	lung
7	chr1:180627600-180640000	Weak transcription	Fetal Heart	heart
8	chr1:180627800-180634200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:180628200-180631600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:180629200-180633800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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