Variant report

Variant	rs1000449
Chromosome Location	chr14:71707567-71707568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1000448	0.99[ASN][1000 genomes]
rs11158903	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11622499	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11623545	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs11627275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190863	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4899392	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs56398258	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7149082	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1000449	PLEKHH1	cis	cerebellum	SCAN
rs1000449	PCNX	cis	cerebellum	SCAN
rs1000449	ACOT1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71695800-71709400	Weak transcription	Pancreas	Pancrea
2	chr14:71703000-71709000	Weak transcription	Right Atrium	heart
3	chr14:71703200-71708600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:71703400-71708400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:71703400-71709000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:71704600-71707600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:71704600-71713200	Weak transcription	Thymus	Thymus
8	chr14:71705800-71708200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr14:71705800-71708200	Weak transcription	NHDF-Ad	bronchial
10	chr14:71706000-71709000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:71706800-71707600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:71706800-71707600	Active TSS	Fetal Brain Male	brain
13	chr14:71706800-71707600	Enhancers	Fetal Thymus	thymus
14	chr14:71706800-71708400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr14:71706800-71708600	Enhancers	Spleen	Spleen
16	chr14:71706800-71709600	Enhancers	Fetal Lung	lung
17	chr14:71706800-71711800	Enhancers	Fetal Heart	heart
18	chr14:71706800-71713000	Enhancers	Fetal Muscle Leg	muscle
19	chr14:71707000-71707800	Enhancers	HSMM	muscle
20	chr14:71707200-71707600	Enhancers	Primary T cells from cord blood	blood
21	chr14:71707200-71708200	Enhancers	NHEK	skin
22	chr14:71707200-71708600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:71707200-71712000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr14:71707200-71712000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr14:71707400-71707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:71707400-71708200	Weak transcription	Esophagus	oesophagus
27	chr14:71707400-71708600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr14:71707400-71712000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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