Variant report

Variant	rs6658312
Chromosome Location	chr1:62762267-62762268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10157938	0.83[ASN][1000 genomes]
rs10465842	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889318	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12749514	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325740	0.89[ASN][1000 genomes]
rs1886833	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886834	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925827	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366207	0.98[ASN][1000 genomes]
rs2477874	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666509	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2765266	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765268	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765269	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35126231	0.98[ASN][1000 genomes]
rs3850632	0.85[AMR][1000 genomes]
rs4915606	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587966	0.87[ASN][1000 genomes]
rs6675508	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6675627	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7514266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881548	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
3	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:62756400-62764800	Weak transcription	HepG2	liver
5	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
9	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:62760800-62762400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:62761000-62762400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:62761000-62762400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:62761000-62762400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:62761000-62763200	Enhancers	Fetal Stomach	stomach
15	chr1:62761200-62762400	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:62761200-62762400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr1:62761200-62762400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:62761200-62762400	Enhancers	Brain Anterior Caudate	brain
19	chr1:62761200-62762400	Enhancers	Brain Germinal Matrix	brain
20	chr1:62761200-62762600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:62761200-62763200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:62761400-62762400	Enhancers	Brain Substantia Nigra	brain
23	chr1:62761600-62762400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:62761600-62762600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:62761800-62765000	Weak transcription	Fetal Kidney	kidney
26	chr1:62761800-62767200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:62762000-62762400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:62762000-62764800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:62762000-62765000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:62762000-62765400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:62762000-62765600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:62762000-62766000	Weak transcription	Brain Angular Gyrus	brain
33	chr1:62762000-62767000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:62762200-62762400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:62762200-62762400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:62762200-62762400	Enhancers	Adipose Nuclei	Adipose
37	chr1:62762200-62762400	Enhancers	Brain Hippocampus Middle	brain
38	chr1:62762200-62762600	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:62762200-62762800	Enhancers	Fetal Muscle Trunk	muscle
40	chr1:62762200-62763800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:62762200-62763800	Weak transcription	NHEK	skin
42	chr1:62762200-62764200	Weak transcription	Pancreas	Pancrea
43	chr1:62762200-62764200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:62762200-62765000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:62762200-62765000	Weak transcription	Fetal Thymus	thymus
46	chr1:62762200-62765000	Weak transcription	Left Ventricle	heart
47	chr1:62762200-62765000	Weak transcription	Right Atrium	heart
48	chr1:62762200-62765000	Weak transcription	HMEC	breast
49	chr1:62762200-62765000	Weak transcription	HSMM	muscle
50	chr1:62762200-62765200	Weak transcription	HSMMtube	muscle

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