Variant report

Variant	rs2888585
Chromosome Location	chr2:39246683-39246684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39246125..39247671-chr2:39262615..39264242,2	K562	blood:
2	chr2:39244399..39247798-chr2:39249250..39251701,4	K562	blood:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10153761	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10165968	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs10166801	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10172085	0.94[EUR][1000 genomes]
rs10172714	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs10177250	1.00[CHB][hapmap]
rs10183915	0.85[CEU][hapmap]
rs10186762	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs10190377	0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs10192250	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs10194374	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201980	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10206751	0.85[CHB][hapmap]
rs1043793	0.92[CHB][hapmap]
rs10439459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10779924	0.82[ASN][1000 genomes]
rs11124659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124660	0.95[EUR][1000 genomes]
rs11692687	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12471731	0.84[CHB][hapmap]
rs12620003	0.84[EUR][1000 genomes]
rs12620071	0.96[EUR][1000 genomes]
rs12622969	0.82[EUR][1000 genomes]
rs12712630	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13023273	0.91[ASN][1000 genomes]
rs13031871	0.80[EUR][1000 genomes]
rs13033392	0.85[EUR][1000 genomes]
rs1377860	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs1377861	0.96[EUR][1000 genomes]
rs1377863	0.96[EUR][1000 genomes]
rs1377864	0.86[CHB][hapmap]
rs1454220	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1454221	0.85[ASN][1000 genomes]
rs1454222	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1454223	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs1454225	0.91[ASN][1000 genomes]
rs1454226	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1454227	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454228	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470914	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs1470915	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840281	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1869513	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1947432	0.91[ASN][1000 genomes]
rs2060987	0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2060988	0.85[CHB][hapmap]
rs2060989	0.96[EUR][1000 genomes]
rs2123876	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2123879	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs2123881	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2123882	0.83[EUR][1000 genomes]
rs2168042	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2278914	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2290445	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs2305516	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2373474	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2373495	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373496	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373497	0.86[CHB][hapmap]
rs2924714	0.96[EUR][1000 genomes]
rs2969763	0.96[EUR][1000 genomes]
rs297120	0.86[CHB][hapmap]
rs297121	0.96[EUR][1000 genomes]
rs297125	0.96[EUR][1000 genomes]
rs297128	0.96[EUR][1000 genomes]
rs297129	0.96[EUR][1000 genomes]
rs297130	0.96[EUR][1000 genomes]
rs297131	0.81[EUR][1000 genomes]
rs297132	0.82[EUR][1000 genomes]
rs297133	0.96[EUR][1000 genomes]
rs297134	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs297136	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297137	0.96[EUR][1000 genomes]
rs297139	0.96[EUR][1000 genomes]
rs297140	0.96[EUR][1000 genomes]
rs297141	0.96[EUR][1000 genomes]
rs297142	0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs297143	0.96[EUR][1000 genomes]
rs297144	0.86[CHB][hapmap]
rs297145	0.82[EUR][1000 genomes]
rs297147	0.82[EUR][1000 genomes]
rs297148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes]
rs297149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs297150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs297151	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs297152	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs297153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs297155	0.80[EUR][1000 genomes]
rs297156	0.84[EUR][1000 genomes]
rs297157	0.96[EUR][1000 genomes]
rs297158	0.87[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs297159	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs297160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs366840	0.82[EUR][1000 genomes]
rs3765058	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs378698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs3796038	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs388958	0.82[EUR][1000 genomes]
rs4142729	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs422854	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap]
rs4643520	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4670269	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs4670270	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4670272	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670903	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4670905	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4670907	0.86[ASN][1000 genomes]
rs57378308	0.95[EUR][1000 genomes]
rs58645871	0.89[EUR][1000 genomes]
rs59732351	0.95[EUR][1000 genomes]
rs61405040	0.96[EUR][1000 genomes]
rs6419600	0.82[EUR][1000 genomes]
rs6544183	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs6544185	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs6544191	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6544194	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544195	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes]
rs6704656	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs6713281	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6716101	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs6725356	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6725644	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739568	0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6752850	0.89[ASN][1000 genomes]
rs6756184	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72909662	0.95[EUR][1000 genomes]
rs7568552	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7571052	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7577088	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9309031	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs963730	0.83[CHB][hapmap]
rs963731	0.84[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs9679498	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs970409	0.96[EUR][1000 genomes]
rs997344	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[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
rs2888585	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	chr2:39211000-39247600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:39213400-39251200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39213400-39259800	Weak transcription	Right Ventricle	heart
4	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
5	chr2:39219000-39259200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
7	chr2:39229000-39251400	Weak transcription	Fetal Heart	heart
8	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:39235400-39249600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:39235600-39247600	Weak transcription	HSMMtube	muscle
13	chr2:39235600-39251800	Weak transcription	NHEK	skin
14	chr2:39235600-39259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:39235600-39259800	Weak transcription	Spleen	Spleen
16	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
17	chr2:39235600-39295800	Weak transcription	NHLF	lung
18	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
19	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
20	chr2:39235800-39249600	Weak transcription	Thymus	Thymus
21	chr2:39235800-39257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:39236000-39247600	Weak transcription	Left Ventricle	heart
25	chr2:39236000-39249600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:39236000-39260000	Weak transcription	Hela-S3	cervix
27	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
28	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:39236000-39305600	Weak transcription	Gastric	stomach
30	chr2:39236200-39305600	Weak transcription	Lung	lung
31	chr2:39236400-39263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:39237000-39260200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:39237600-39257600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:39237800-39249800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:39238400-39256400	Weak transcription	Fetal Intestine Small	intestine
36	chr2:39238400-39260600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:39238600-39256400	Weak transcription	Fetal Stomach	stomach
38	chr2:39239200-39249600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:39239400-39249600	Weak transcription	HUVEC	blood vessel
40	chr2:39239400-39254600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:39240400-39249400	Weak transcription	HMEC	breast
42	chr2:39240400-39250800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:39240600-39249600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:39240600-39249600	Weak transcription	Primary T cells from cord blood	blood
45	chr2:39240600-39249600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:39240800-39249400	Weak transcription	Osteobl	bone
47	chr2:39240800-39249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:39240800-39249600	Weak transcription	K562	blood
49	chr2:39240800-39249800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:39240800-39251400	Weak transcription	Muscle Satellite Cultured Cells	--

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