Variant report

Variant	rs16851752
Chromosome Location	chr3:141484778-141484779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1055690	0.82[JPT][hapmap]
rs11542226	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16851704	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs16851717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851763	0.88[CHB][hapmap]
rs1879284	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879285	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980192	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3773840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588340	1.00[CEU][hapmap]
rs57394236	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57805567	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57983026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58115387	0.83[EUR][1000 genomes]
rs58300294	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59998648	0.86[EUR][1000 genomes]
rs60938827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61278509	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61294533	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61632965	0.86[EUR][1000 genomes]
rs6783647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73872318	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872319	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73872322	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73872326	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7632069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635763	0.82[JPT][hapmap]
rs7642922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643689	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9789959	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9789973	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790069	1.00[CHB][hapmap]
rs9790073	1.00[CHB][hapmap]
rs9790075	0.88[ASN][1000 genomes]

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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16851752	RNF7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141461800-141498200	Weak transcription	Right Ventricle	heart
2	chr3:141470000-141486400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:141472000-141500800	Weak transcription	Thymus	Thymus
4	chr3:141472600-141484800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:141482400-141485800	Weak transcription	Gastric	stomach
6	chr3:141482400-141488200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:141482600-141487200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:141483000-141484800	Enhancers	Fetal Kidney	kidney
9	chr3:141483400-141485000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:141483400-141487200	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:141483400-141487600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:141483400-141488000	Weak transcription	K562	blood
13	chr3:141484200-141488000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:141484400-141485400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:141484400-141486200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:141484400-141486400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:141484400-141486800	Weak transcription	Lung	lung
18	chr3:141484600-141487600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links