Variant report

Variant	rs6717116
Chromosome Location	chr2:133539460-133539461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10187405	0.89[EUR][1000 genomes]
rs10191147	0.81[YRI][hapmap]
rs1025388	0.84[EUR][1000 genomes]
rs1025389	0.87[EUR][1000 genomes]
rs12611515	0.86[YRI][hapmap]
rs12616282	0.87[EUR][1000 genomes]
rs12691828	0.81[JPT][hapmap]
rs12691829	0.82[EUR][1000 genomes]
rs12691830	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4953988	0.85[EUR][1000 genomes]
rs4953990	0.92[CEU][hapmap]
rs56318788	0.90[EUR][1000 genomes]
rs6430374	0.84[EUR][1000 genomes]
rs6708285	0.87[EUR][1000 genomes]
rs6713570	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6730282	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747173	0.82[YRI][hapmap]
rs7557503	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs7568532	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs7592077	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605691	0.88[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1002955	chr2:133440142-133743211	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv834379	chr2:133471980-133665601	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133517600-133539800	Weak transcription	Brain Substantia Nigra	brain
2	chr2:133519800-133539800	Weak transcription	Fetal Stomach	stomach
3	chr2:133523400-133544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:133524200-133547800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:133527600-133544200	Weak transcription	Left Ventricle	heart
6	chr2:133528000-133541800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:133529000-133540000	Weak transcription	Brain Anterior Caudate	brain
8	chr2:133529000-133540200	Weak transcription	Lung	lung
9	chr2:133529400-133540600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:133529400-133544400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:133530600-133539600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:133530800-133539800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:133530800-133542600	Weak transcription	Ovary	ovary
14	chr2:133530800-133554400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:133531000-133539800	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:133531400-133561400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:133532600-133542000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:133533200-133547000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:133537000-133542600	Weak transcription	Fetal Brain Male	brain
20	chr2:133537200-133540400	Weak transcription	Fetal Brain Female	brain
21	chr2:133538200-133540600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:133538200-133543800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:133538200-133561200	Weak transcription	Hela-S3	cervix
24	chr2:133538400-133540000	Strong transcription	Liver	Liver
25	chr2:133538400-133543200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:133538800-133541600	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:133538800-133553800	Weak transcription	Right Ventricle	heart
28	chr2:133539400-133539600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:133539400-133539600	Enhancers	Brain Angular Gyrus	brain
30	chr2:133539400-133540200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:133539400-133540400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr2:133539400-133540600	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:133539400-133541000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links