Variant report

Variant	rs11130211
Chromosome Location	chr3:49645209-49645210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1009051	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10452032	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1078341	0.94[CEU][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10865956	0.80[YRI][hapmap]
rs11130207	0.84[AMR][1000 genomes]
rs11130208	1.00[CEU][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130217	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs11709734	0.94[CEU][hapmap]
rs11720705	0.94[CEU][hapmap]
rs11721148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928090	1.00[CHB][hapmap]
rs12583	0.80[YRI][hapmap]
rs12637313	0.94[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12715437	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs13096480	0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1352889	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464569	1.00[CHB][hapmap]
rs1491983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491985	0.94[CEU][hapmap]
rs1532204	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1586827	0.94[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1982861	0.80[YRI][hapmap]
rs2029591	1.00[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131108	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2312462	0.80[YRI][hapmap]
rs2329021	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3020779	0.94[CEU][hapmap];0.81[YRI][hapmap]
rs34890793	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs3866330	1.00[CHB][hapmap]
rs3905330	1.00[CHB][hapmap]
rs4241405	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4241407	1.00[CHB][hapmap];0.80[YRI][hapmap]
rs4855833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855845	0.94[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855846	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855848	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855849	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4855882	0.94[CEU][hapmap]
rs4855885	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs62262672	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62262673	0.84[EUR][1000 genomes]
rs62262675	0.85[EUR][1000 genomes]
rs6446284	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6446286	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6774202	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6797299	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6809879	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap]
rs7613603	0.94[CEU][hapmap]
rs7620848	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs7622786	1.00[ASN][1000 genomes]
rs7628207	0.94[CEU][hapmap]
rs7637711	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs7653505	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs940045	1.00[CHB][hapmap]
rs9824435	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs9829155	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs9830730	0.94[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9835157	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs9849038	0.94[CEU][hapmap]
rs9862534	1.00[CHB][hapmap]
rs9870755	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs9870858	0.94[CEU][hapmap]
rs9883000	0.94[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11130211	HEMK	cis	multi-tissue	Pritchard
rs11130211	AMT	cis	Nerve Tibial	GTEx
rs11130211	NICN1	cis	Thyroid	GTEx
rs11130211	AMT	cis	Thyroid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:49640400-49646800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:49640800-49646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49643800-49645400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr3:49643800-49645400	Enhancers	Stomach Mucosa	stomach
9	chr3:49643800-49645800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:49644000-49645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:49644000-49645400	Enhancers	Brain Hippocampus Middle	brain
12	chr3:49644000-49645400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:49644000-49645400	Enhancers	Esophagus	oesophagus
14	chr3:49644200-49645600	Enhancers	Hela-S3	cervix
15	chr3:49644200-49646800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:49644400-49645400	Enhancers	Right Ventricle	heart
17	chr3:49644400-49645400	Enhancers	HMEC	breast
18	chr3:49644400-49645400	Enhancers	NHEK	skin
19	chr3:49644600-49645400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49644600-49645400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:49644600-49645400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:49644800-49645400	Enhancers	Brain Germinal Matrix	brain
24	chr3:49644800-49645600	Enhancers	Brain Angular Gyrus	brain
25	chr3:49644800-49645600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:49645000-49645800	Enhancers	Brain Substantia Nigra	brain
27	chr3:49645000-49646800	Weak transcription	Fetal Brain Female	brain
28	chr3:49645000-49646800	Weak transcription	Fetal Stomach	stomach
29	chr3:49645000-49647200	Weak transcription	Left Ventricle	heart
30	chr3:49645200-49646800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49645200-49646800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:49645200-49646800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:49645200-49647000	Weak transcription	Fetal Brain Male	brain

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