Variant report

Variant	rs828054
Chromosome Location	chr1:97610026-97610027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10430074	1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs10875054	1.00[ASN][1000 genomes]
rs10875055	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12063966	0.82[YRI][hapmap]
rs12066847	0.82[YRI][hapmap]
rs12127420	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12133667	1.00[CHB][hapmap]
rs1413227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1413229	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs1413231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1413235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs17471125	1.00[CHB][hapmap]
rs1970142	1.00[ASN][1000 genomes]
rs28619552	1.00[ASN][1000 genomes]
rs3762412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs494271	1.00[CHB][hapmap]
rs4949945	1.00[ASN][1000 genomes]
rs4950023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs496179	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs533365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs595937	1.00[ASN][1000 genomes]
rs6593632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6593635	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6593636	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6593637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6661442	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6673282	1.00[ASN][1000 genomes]
rs6681752	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6683351	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6683883	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6692424	1.00[ASN][1000 genomes]
rs6693034	1.00[ASN][1000 genomes]
rs6697132	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6700957	1.00[ASN][1000 genomes]
rs67665424	1.00[ASN][1000 genomes]
rs688913	1.00[ASN][1000 genomes]
rs7513333	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs7528359	1.00[ASN][1000 genomes]
rs7531100	1.00[ASN][1000 genomes]
rs7537668	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs7545506	1.00[ASN][1000 genomes]
rs828052	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828058	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs885622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs914959	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830692	chr1:97501492-97625153	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97563600-97619200	Weak transcription	Dnd41	blood
2	chr1:97564200-97632800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:97585600-97621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:97597400-97619600	Weak transcription	Liver	Liver
5	chr1:97603400-97610200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:97604000-97620000	Weak transcription	Pancreas	Pancrea
7	chr1:97604200-97610400	Weak transcription	Fetal Brain Male	brain
8	chr1:97604400-97611000	Weak transcription	Stomach Mucosa	stomach
9	chr1:97604400-97614800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:97604400-97629000	Weak transcription	Primary B cells from cord blood	blood
11	chr1:97604600-97610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:97604600-97614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:97606200-97610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:97606200-97626600	Weak transcription	Ovary	ovary
15	chr1:97606800-97610400	Weak transcription	Primary T cells from cord blood	blood
16	chr1:97606800-97610400	Weak transcription	Aorta	Aorta
17	chr1:97607200-97611000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:97607400-97612600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:97608000-97610200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:97608600-97610200	Enhancers	Brain Substantia Nigra	brain
21	chr1:97608800-97610400	Enhancers	Osteobl	bone
22	chr1:97608800-97611200	Enhancers	NHEK	skin
23	chr1:97608800-97611400	Enhancers	Hela-S3	cervix
24	chr1:97608800-97611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:97608800-97612000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:97608800-97612000	Enhancers	HMEC	breast
27	chr1:97608800-97612200	Enhancers	Brain Anterior Caudate	brain
28	chr1:97608800-97612200	Enhancers	NHDF-Ad	bronchial
29	chr1:97608800-97612400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:97609000-97610400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:97609000-97610400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:97609000-97610600	Enhancers	Brain Hippocampus Middle	brain
33	chr1:97609000-97611000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:97609000-97611200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:97609000-97611600	Enhancers	HSMM	muscle
36	chr1:97609000-97612000	Enhancers	NHLF	lung
37	chr1:97609200-97611600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:97609200-97612000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:97609200-97612800	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:97609200-97627800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:97609400-97611400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr1:97609400-97612000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:97609400-97612400	Enhancers	HUVEC	blood vessel
44	chr1:97609600-97611000	Flanking Active TSS	NH-A	brain
45	chr1:97609600-97611200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:97609600-97611200	Enhancers	HSMMtube	muscle
47	chr1:97609800-97610600	Enhancers	Brain Angular Gyrus	brain
48	chr1:97609800-97612000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:97609800-97612600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:97610000-97610400	Enhancers	Muscle Satellite Cultured Cells	--

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