Variant report

Variant	rs4844496
Chromosome Location	chr1:210030755-210030756
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210023266..210025244-chr1:210030521..210032417,2	MCF-7	breast:
2	chr1:209999584..210001298-chr1:210028865..210031163,2	K562	blood:
3	chr1:210022253..210024519-chr1:210030671..210033538,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10863790	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119345	0.81[AMR][1000 genomes]
rs11119346	0.93[EUR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119359	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12058100	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12063989	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12064085	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12064211	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12066340	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12075674	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12078157	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.86[EUR][1000 genomes]
rs12405750	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015217	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17015255	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17015268	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2069068	0.93[EUR][1000 genomes]
rs2076149	1.00[AFR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes]
rs2235371	0.86[GIH][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2235377	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs3753517	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4844491	1.00[AFR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844498	0.85[AMR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57283682	1.00[AFR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4844496	SNORD117	trans	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
4	chr1:210017600-210041200	Weak transcription	Fetal Brain Male	brain
5	chr1:210018000-210032800	Weak transcription	Small Intestine	intestine
6	chr1:210019000-210033800	Weak transcription	Fetal Heart	heart
7	chr1:210025000-210035800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:210026200-210033200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:210026200-210035400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:210026200-210035600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:210027600-210032200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:210027600-210032400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:210027600-210034200	Weak transcription	HMEC	breast
14	chr1:210027600-210034600	Weak transcription	K562	blood
15	chr1:210027600-210036200	Weak transcription	Fetal Lung	lung
16	chr1:210027600-210036800	Weak transcription	HSMM	muscle
17	chr1:210027800-210031200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:210027800-210031800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:210027800-210032800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:210027800-210034200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:210027800-210034400	Weak transcription	NH-A	brain
22	chr1:210027800-210034800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:210027800-210035000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:210027800-210035400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:210028000-210031200	Weak transcription	Fetal Thymus	thymus
26	chr1:210028000-210031400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:210028000-210031400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:210028000-210031600	Weak transcription	Aorta	Aorta
29	chr1:210028000-210031600	Weak transcription	Left Ventricle	heart
30	chr1:210028000-210032200	Weak transcription	GM12878-XiMat	blood
31	chr1:210028000-210033000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:210028000-210033000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:210028000-210033000	Weak transcription	HUVEC	blood vessel
34	chr1:210028000-210033200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:210028000-210033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:210028000-210034000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:210028000-210034200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:210028000-210036200	Weak transcription	HSMMtube	muscle
39	chr1:210028200-210031400	Weak transcription	Psoas Muscle	Psoas
40	chr1:210028200-210031600	Weak transcription	Colonic Mucosa	Colon
41	chr1:210028200-210032000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:210028200-210032000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:210028200-210032600	Weak transcription	Pancreas	Pancrea
44	chr1:210028200-210033200	Weak transcription	NHLF	lung
45	chr1:210028200-210033600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:210028200-210034200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:210028200-210036400	Weak transcription	Hela-S3	cervix
48	chr1:210028200-210042400	Weak transcription	NHDF-Ad	bronchial
49	chr1:210028400-210031000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:210028400-210034200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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