Variant report

Variant	rs4695923
Chromosome Location	chr4:175254461-175254462
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPGD-2	chr4:175254458-175254509	ucscGeneNc_uc003ito_1

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10565	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11934405	0.86[ASN][1000 genomes]
rs11939414	0.85[ASN][1000 genomes]
rs11944262	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946084	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111067	0.93[ASN][1000 genomes]
rs13112711	0.93[ASN][1000 genomes]
rs13130276	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17294597	1.00[CHB][hapmap]
rs34066344	0.85[ASN][1000 genomes]
rs34274380	0.85[ASN][1000 genomes]
rs34369193	0.85[ASN][1000 genomes]
rs34698083	0.85[ASN][1000 genomes]
rs34765808	0.85[ASN][1000 genomes]
rs34988464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35377027	0.85[ASN][1000 genomes]
rs35918158	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4280712	0.85[ASN][1000 genomes]
rs4287982	0.80[EUR][1000 genomes]
rs4293767	0.85[ASN][1000 genomes]
rs4408938	0.85[ASN][1000 genomes]
rs4408939	0.85[ASN][1000 genomes]
rs4695922	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4695926	0.85[ASN][1000 genomes]
rs4695927	0.85[ASN][1000 genomes]
rs4695928	0.85[ASN][1000 genomes]
rs67509565	0.85[ASN][1000 genomes]
rs6812756	0.85[ASN][1000 genomes]
rs6812772	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6817902	0.85[ASN][1000 genomes]

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	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4695923	KIAA1712	cis	multi-tissue	Pritchard
rs4695923	CEP44	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
2	chr4:175233800-175255800	Weak transcription	Fetal Intestine Large	intestine
3	chr4:175236200-175258400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:175238000-175254800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:175238000-175255400	Weak transcription	Primary B cells from cord blood	blood
6	chr4:175241400-175257400	Weak transcription	Fetal Thymus	thymus
7	chr4:175246400-175261800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:175249000-175257000	Weak transcription	Aorta	Aorta
9	chr4:175252800-175255000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:175253400-175256800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:175253400-175256800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:175253600-175256800	Enhancers	NHEK	skin
13	chr4:175253800-175256600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:175254000-175254600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:175254200-175254800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:175254200-175255600	Weak transcription	HMEC	breast

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