Variant report

Variant	rs55825882
Chromosome Location	chr1:179106973-179106974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004959	0.81[ASN][1000 genomes]
rs10157885	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10158768	0.88[ASN][1000 genomes]
rs12080991	0.83[ASN][1000 genomes]
rs12143004	0.84[ASN][1000 genomes]
rs17277358	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361990	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17362128	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274228	0.85[ASN][1000 genomes]
rs2274230	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636281	0.82[AFR][1000 genomes]
rs2793806	0.80[AFR][1000 genomes]
rs2816210	0.80[AFR][1000 genomes]
rs28459842	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28913571	0.83[AFR][1000 genomes]
rs28913879	0.83[AFR][1000 genomes]
rs28914474	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28914485	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753532	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45499094	0.85[ASN][1000 genomes]
rs55642919	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55827544	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955319	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56382583	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58082966	0.92[AFR][1000 genomes]
rs60741626	0.86[ASN][1000 genomes]
rs60826716	0.86[ASN][1000 genomes]
rs6668200	0.97[EUR][1000 genomes]
rs6669988	0.86[ASN][1000 genomes]
rs74131923	0.83[AFR][1000 genomes]
rs9650996	0.92[AFR][1000 genomes]
rs9650997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650998	0.97[EUR][1000 genomes]
rs9724754	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9730271	0.88[ASN][1000 genomes]
rs9803885	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
2	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
3	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:179091000-179108800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
8	chr1:179095800-179107400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:179096400-179108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:179096600-179110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:179098200-179112000	Weak transcription	Lung	lung
12	chr1:179099200-179110200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:179099200-179110400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:179099200-179110400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:179099200-179114800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:179099400-179107000	Weak transcription	Placenta	Placenta
17	chr1:179099400-179110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:179099400-179110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:179099400-179112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:179099400-179112000	Weak transcription	Left Ventricle	heart
21	chr1:179099600-179109200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:179099600-179109800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:179099600-179109800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:179099600-179110000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:179099600-179110200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:179099600-179110600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:179099600-179110800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
29	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:179099800-179107000	Weak transcription	Adipose Nuclei	Adipose
32	chr1:179099800-179107000	Weak transcription	Psoas Muscle	Psoas
33	chr1:179099800-179108800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:179099800-179109400	Weak transcription	Primary B cells from cord blood	blood
35	chr1:179099800-179111800	Weak transcription	HepG2	liver
36	chr1:179100000-179108600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:179100000-179121000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:179100200-179110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:179100600-179110800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:179100600-179112000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:179100600-179117200	Weak transcription	Fetal Intestine Small	intestine
42	chr1:179100800-179107000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:179100800-179107000	Weak transcription	HMEC	breast
44	chr1:179100800-179110400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:179100800-179110400	Weak transcription	K562	blood
46	chr1:179101000-179109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:179101000-179110000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:179103400-179107000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:179106000-179108600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:179106200-179107000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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