Variant report

Variant	rs6795140
Chromosome Location	chr3:24061129-24061130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:24060176..24062310-chr3:24299277..24301761,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10865793	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11129132	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713946	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714202	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12488759	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1397881	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1511543	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17014043	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1949121	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001209	0.81[CHB][hapmap]
rs2063480	0.82[JPT][hapmap]
rs2089849	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2360958	0.82[JPT][hapmap]
rs2360959	0.88[JPT][hapmap]
rs34288805	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3856622	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4277632	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4297994	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4356765	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4502534	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4561770	0.82[JPT][hapmap]
rs4568061	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4624512	0.89[JPT][hapmap]
rs4858573	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858574	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6550834	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550835	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6550836	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6765461	0.89[JPT][hapmap]
rs7372302	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431278	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7431344	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7623641	0.82[JPT][hapmap]
rs7634184	0.83[JPT][hapmap]
rs7646501	0.88[ASN][1000 genomes]
rs951015	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs954734	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9863605	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv834639	chr3:24037113-24233925	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv536523	chr3:24041166-24076110	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6795140	NR1D2	cis	Temporal Cortex	GTEx
rs6795140	NR1D2	cis	Brain Pons	GTEx
rs6795140	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24053600-24065000	Weak transcription	Psoas Muscle	Psoas
2	chr3:24058600-24064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:24060200-24061200	Flanking Active TSS	NHEK	skin
4	chr3:24060200-24062000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:24060400-24061600	Enhancers	Gastric	stomach
6	chr3:24060600-24061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:24060800-24061400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:24060800-24061400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:24060800-24062000	Enhancers	Esophagus	oesophagus
10	chr3:24061000-24061200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:24061000-24061800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:24061000-24069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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