Variant report

Variant	rs1454223
Chromosome Location	chr2:39224351-39224352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39219746..39222120-chr2:39223877..39225648,2	K562	blood:
2	chr2:39219470..39222120-chr2:39223877..39225379,2	K562	blood:

Variant related genes	Relation type
ENSG00000229692	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10153761	0.91[ASN][1000 genomes]
rs10165968	0.83[GIH][hapmap]
rs10166801	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10172714	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10177250	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10183915	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10186762	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194374	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10201980	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1043793	0.92[CHB][hapmap]
rs10439459	0.94[ASN][1000 genomes]
rs10779924	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11124659	0.95[ASN][1000 genomes]
rs11692687	0.91[ASN][1000 genomes]
rs12471731	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712630	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs13023273	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031871	0.87[CHD][hapmap]
rs1377860	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap]
rs1454220	0.85[ASN][1000 genomes]
rs1454221	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1454222	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1454225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454226	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1454227	0.93[ASN][1000 genomes]
rs1454228	0.92[ASN][1000 genomes]
rs1470915	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[ASN][1000 genomes]
rs1840281	0.91[ASN][1000 genomes]
rs1869513	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869514	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1947432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1947433	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2060987	0.84[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs2060988	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs2123876	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2123879	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2123881	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2168042	0.84[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2168044	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278912	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2278913	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278914	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2373474	0.93[ASN][1000 genomes]
rs2373495	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2373496	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2603145	0.84[AMR][1000 genomes]
rs2888585	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs297120	0.83[GIH][hapmap]
rs297124	0.83[GIH][hapmap]
rs297135	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs297142	0.83[GIH][hapmap]
rs297148	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs297149	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs297150	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs297151	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs297152	0.87[CEU][hapmap]
rs297153	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs297158	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs297159	1.00[CEU][hapmap]
rs297160	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs371745	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3765058	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs378698	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4142729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422854	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4643520	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670269	0.87[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670270	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670272	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4670901	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4670903	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670904	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4670905	0.90[ASN][1000 genomes]
rs4670907	0.80[ASN][1000 genomes]
rs6544183	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6544184	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6544185	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6544186	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6544187	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6544194	0.85[ASN][1000 genomes]
rs6544195	0.85[ASN][1000 genomes]
rs6544197	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs6704656	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[ASN][1000 genomes]
rs6716101	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6725356	1.00[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs6725644	0.93[ASN][1000 genomes]
rs6739568	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6752850	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6755527	0.92[AMR][1000 genomes]
rs6756184	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6758330	0.82[CHD][hapmap]
rs7568552	0.80[ASN][1000 genomes]
rs7571052	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7573310	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7577088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7594644	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309031	0.93[ASN][1000 genomes]
rs958412	0.83[AMR][1000 genomes]
rs963730	1.00[CHB][hapmap]
rs963731	1.00[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs9679498	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs997344	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[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	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1454223	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39197000-39225800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:39200800-39227800	Weak transcription	Fetal Heart	heart
3	chr2:39202400-39225600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:39202400-39228800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:39205800-39242600	Weak transcription	Psoas Muscle	Psoas
6	chr2:39206000-39235800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:39207600-39224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:39209800-39224400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:39210000-39232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:39210400-39224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:39210400-39233200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:39210400-39241600	Strong transcription	Adipose Nuclei	Adipose
13	chr2:39210400-39242600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:39210600-39229400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:39210600-39242400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:39210800-39224800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:39210800-39230200	Strong transcription	Dnd41	blood
18	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:39211200-39224800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:39211200-39228600	Strong transcription	HepG2	liver
21	chr2:39211400-39237800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:39211600-39242000	Weak transcription	Stomach Mucosa	stomach
23	chr2:39211800-39231200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:39211800-39239600	Strong transcription	Fetal Intestine Large	intestine
25	chr2:39213400-39225600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:39213400-39225600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:39213400-39225800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:39213400-39225800	Weak transcription	Fetal Brain Female	brain
29	chr2:39213400-39225800	Weak transcription	Spleen	Spleen
30	chr2:39213400-39226400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:39213400-39226800	Weak transcription	Aorta	Aorta
32	chr2:39213400-39228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:39213400-39228800	Weak transcription	Brain Angular Gyrus	brain
34	chr2:39213400-39234400	Weak transcription	Gastric	stomach
35	chr2:39213400-39234400	Weak transcription	NHEK	skin
36	chr2:39213400-39242200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:39213400-39242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
40	chr2:39213800-39225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:39213800-39226200	Weak transcription	K562	blood
42	chr2:39213800-39228200	Weak transcription	Fetal Intestine Small	intestine
43	chr2:39213800-39235000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:39213800-39235000	Weak transcription	Small Intestine	intestine
45	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
46	chr2:39214200-39235400	Weak transcription	Hela-S3	cervix
47	chr2:39214800-39224800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:39214800-39225600	Weak transcription	HSMMtube	muscle
49	chr2:39217400-39229000	Strong transcription	Liver	Liver
50	chr2:39217400-39241800	Strong transcription	Primary T cells fromperipheralblood	blood

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