Variant report

Variant	rs11124679
Chromosome Location	chr2:39598108-39598109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39596692..39599194-chr2:39603552..39605779,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10153665	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10169391	0.85[AFR][1000 genomes]
rs10170424	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10170604	0.94[AFR][1000 genomes]
rs10170617	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10172736	0.86[EUR][1000 genomes]
rs10173556	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10175038	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10175333	0.89[AFR][1000 genomes]
rs10181650	0.90[AFR][1000 genomes]
rs10190069	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10195629	0.83[EUR][1000 genomes]
rs1035232	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10865149	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10865150	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10865152	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124668	0.86[EUR][1000 genomes]
rs11124673	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124676	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11124677	0.88[AFR][1000 genomes]
rs11124681	0.86[AFR][1000 genomes]
rs1125839	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11688728	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1211996	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622941	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12712636	0.84[EUR][1000 genomes]
rs12712641	0.94[AFR][1000 genomes]
rs13028561	0.90[AFR][1000 genomes]
rs1468902	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1474424	0.93[AFR][1000 genomes]
rs1477164	0.93[AFR][1000 genomes]
rs17023837	0.89[EUR][1000 genomes]
rs1861735	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1922827	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2005892	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2056654	0.89[AFR][1000 genomes]
rs2111382	0.81[AFR][1000 genomes]
rs2178762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2193422	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373534	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2373535	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2373536	0.90[AFR][1000 genomes]
rs2542008	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888594	0.96[EUR][1000 genomes]
rs2888598	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755177	0.90[EUR][1000 genomes]
rs3755178	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3770670	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3770675	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3770678	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4670934	0.89[AFR][1000 genomes]
rs4670935	0.89[AFR][1000 genomes]
rs4670936	0.88[AFR][1000 genomes]
rs6419603	0.93[AFR][1000 genomes]
rs6544213	0.86[EUR][1000 genomes]
rs6544220	0.82[EUR][1000 genomes]
rs6544222	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544223	0.93[AFR][1000 genomes]
rs6544224	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6544228	0.89[AFR][1000 genomes]
rs6712274	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6712921	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6717792	0.84[AFR][1000 genomes]
rs6718134	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6724393	0.90[AFR][1000 genomes]
rs6725938	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6730902	0.89[AFR][1000 genomes]
rs6732611	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6736700	0.85[EUR][1000 genomes]
rs6741019	0.86[EUR][1000 genomes]
rs6742170	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6743041	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6753323	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6756183	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6759495	0.89[AFR][1000 genomes]
rs6760382	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72801478	0.83[ASN][1000 genomes]
rs7568561	0.81[AMR][1000 genomes]
rs7574250	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7578136	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7579414	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7582160	0.93[AFR][1000 genomes]
rs7591102	0.83[AFR][1000 genomes]
rs7595041	0.90[AFR][1000 genomes]
rs759589	0.92[EUR][1000 genomes]
rs7600014	0.90[EUR][1000 genomes]
rs7600046	0.90[EUR][1000 genomes]
rs7601700	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7603337	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7603392	0.89[AFR][1000 genomes]
rs7604047	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7608153	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11124679	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39584400-39598400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
3	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
4	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:39588000-39607800	Weak transcription	Ovary	ovary
7	chr2:39588000-39608800	Weak transcription	Lung	lung
8	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
10	chr2:39588200-39599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:39588200-39602800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:39588200-39603000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:39588400-39603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:39588600-39599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:39590000-39604800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:39590200-39598200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:39590200-39598400	Weak transcription	Fetal Lung	lung
18	chr2:39590200-39599800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:39590200-39602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:39590200-39602800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:39590200-39604800	Weak transcription	HSMMtube	muscle
22	chr2:39590400-39598200	Weak transcription	Primary B cells from cord blood	blood
23	chr2:39590400-39599800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:39590400-39600400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:39590400-39602400	Weak transcription	Liver	Liver
26	chr2:39590600-39598200	Weak transcription	Fetal Intestine Large	intestine
27	chr2:39590600-39598200	Weak transcription	HSMM	muscle
28	chr2:39590600-39598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39590600-39598600	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:39590600-39601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:39590600-39601200	Weak transcription	Fetal Stomach	stomach
32	chr2:39590600-39602200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:39591000-39602000	Weak transcription	Fetal Thymus	thymus
34	chr2:39591800-39602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:39591800-39604600	Weak transcription	NH-A	brain
36	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:39592000-39606800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:39592200-39599800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:39592400-39599800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:39592400-39600200	Weak transcription	A549	lung
41	chr2:39592400-39604600	Weak transcription	Fetal Heart	heart
42	chr2:39592600-39607000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:39593400-39603200	Weak transcription	K562	blood
45	chr2:39593800-39598200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:39593800-39602800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:39594000-39600800	Weak transcription	Fetal Intestine Small	intestine
48	chr2:39594600-39599600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
50	chr2:39594800-39598800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links