Variant report

Variant	rs961290
Chromosome Location	chr6:53950370-53950371
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10484650	0.84[MEX][hapmap]
rs10948797	1.00[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16884654	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17681477	1.00[JPT][hapmap]
rs2894817	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs526144	0.86[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557018	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581785	0.86[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641426	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673471	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689298	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938357	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73434393	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7742036	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7766702	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs816370	1.00[JPT][hapmap]
rs816371	1.00[JPT][hapmap]
rs9382278	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv7901	chr6:53914491-53981080	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv823691	chr6:53918427-53978766	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv885885	chr6:53920024-54046264	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv34853	chr6:53924697-53977449	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv603120	chr6:53929484-53951857	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv603121	chr6:53929484-53951990	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53941400-53955000	Weak transcription	Right Ventricle	heart
2	chr6:53945000-53970800	Weak transcription	Right Atrium	heart
3	chr6:53948200-53950800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:53948200-53951000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:53948200-53951200	Enhancers	Fetal Heart	heart
6	chr6:53948600-53950400	Weak transcription	Brain Angular Gyrus	brain
7	chr6:53949200-53950800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:53949200-53951400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:53949200-53951400	Enhancers	Adipose Nuclei	Adipose
10	chr6:53949200-53952400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr6:53949400-53951600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:53949600-53950800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:53949600-53952600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:53949600-53953600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr6:53949800-53950600	Enhancers	Left Ventricle	heart
16	chr6:53949800-53950600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr6:53949800-53950800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:53949800-53952400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:53949800-53953200	Enhancers	Fetal Muscle Leg	muscle
20	chr6:53950000-53950400	Enhancers	Brain Anterior Caudate	brain
21	chr6:53950000-53950600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:53950000-53950800	Enhancers	Brain Hippocampus Middle	brain
23	chr6:53950000-53950800	Enhancers	HSMMtube	muscle
24	chr6:53950000-53951000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:53950000-53951000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:53950000-53951000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:53950000-53951000	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:53950000-53951200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:53950000-53951400	Enhancers	Colon Smooth Muscle	Colon
30	chr6:53950000-53952400	Enhancers	Osteobl	bone
31	chr6:53950200-53950400	Active TSS	Psoas Muscle	Psoas
32	chr6:53950200-53950600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:53950200-53950800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:53950200-53951000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:53950200-53951200	Weak transcription	Fetal Stomach	stomach
36	chr6:53950200-53951400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:53950200-53951400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links