Variant report

Variant	rs11124660
Chromosome Location	chr2:39354693-39354694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:39354333-39354753	SK-N-MC	brain:	n/a	n/a
2	MXI1	chr2:39354581-39355654	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39350652..39354915-chr2:39355009..39358498,5	K562	blood:
2	chr2:39351946..39354916-chr2:39358761..39361361,2	K562	blood:

Variant related genes	Relation type
SOS1	TF binding region
ENSG00000202309	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10153761	0.95[EUR][1000 genomes]
rs10165968	0.89[EUR][1000 genomes]
rs10166801	0.93[EUR][1000 genomes]
rs10172085	0.93[EUR][1000 genomes]
rs10177250	0.84[EUR][1000 genomes]
rs10190377	0.84[EUR][1000 genomes]
rs10194374	0.93[EUR][1000 genomes]
rs10200058	0.83[EUR][1000 genomes]
rs10439459	0.95[EUR][1000 genomes]
rs11124659	0.95[EUR][1000 genomes]
rs11692687	0.95[EUR][1000 genomes]
rs12620003	0.89[EUR][1000 genomes]
rs12620071	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622969	0.87[EUR][1000 genomes]
rs12712630	0.81[EUR][1000 genomes]
rs13033392	0.84[EUR][1000 genomes]
rs1377860	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1377861	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1377863	0.95[EUR][1000 genomes]
rs1454220	0.81[EUR][1000 genomes]
rs1454226	0.95[EUR][1000 genomes]
rs1454227	0.82[EUR][1000 genomes]
rs1454228	0.89[EUR][1000 genomes]
rs1470914	0.82[EUR][1000 genomes]
rs1470915	0.95[EUR][1000 genomes]
rs1840281	0.89[EUR][1000 genomes]
rs2060989	0.98[EUR][1000 genomes]
rs2123876	0.91[EUR][1000 genomes]
rs2123879	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2123881	0.95[EUR][1000 genomes]
rs2123882	0.81[EUR][1000 genomes]
rs2168042	0.81[EUR][1000 genomes]
rs2373474	0.93[EUR][1000 genomes]
rs2373495	0.91[EUR][1000 genomes]
rs2373496	0.91[EUR][1000 genomes]
rs2888585	0.95[EUR][1000 genomes]
rs2924714	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2969763	0.98[EUR][1000 genomes]
rs297120	0.83[EUR][1000 genomes]
rs297121	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297122	0.85[ASN][1000 genomes]
rs297124	0.84[EUR][1000 genomes]
rs297125	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297127	0.81[EUR][1000 genomes]
rs297128	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297129	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297130	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297131	0.86[EUR][1000 genomes]
rs297132	0.87[EUR][1000 genomes]
rs297133	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297134	0.87[EUR][1000 genomes]
rs297135	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297136	0.87[EUR][1000 genomes]
rs297137	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs297139	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297140	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297141	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297142	0.87[EUR][1000 genomes]
rs297143	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297144	0.84[EUR][1000 genomes]
rs297145	0.87[EUR][1000 genomes]
rs297147	0.87[EUR][1000 genomes]
rs297148	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs297149	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs297150	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs297151	0.85[EUR][1000 genomes]
rs297152	0.85[EUR][1000 genomes]
rs297153	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs297155	0.82[EUR][1000 genomes]
rs297156	0.85[EUR][1000 genomes]
rs297157	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297158	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297159	0.98[EUR][1000 genomes]
rs297161	0.84[EUR][1000 genomes]
rs366840	0.87[EUR][1000 genomes]
rs378698	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796038	0.82[EUR][1000 genomes]
rs388958	0.87[EUR][1000 genomes]
rs4670272	0.91[EUR][1000 genomes]
rs4670905	0.98[EUR][1000 genomes]
rs57378308	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58645871	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59732351	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61405040	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6419600	0.87[EUR][1000 genomes]
rs6544191	0.98[EUR][1000 genomes]
rs6544194	0.85[EUR][1000 genomes]
rs6544195	0.85[EUR][1000 genomes]
rs6544197	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713281	0.95[EUR][1000 genomes]
rs6725356	0.93[EUR][1000 genomes]
rs6725644	0.93[EUR][1000 genomes]
rs6726833	0.84[EUR][1000 genomes]
rs6739568	0.81[EUR][1000 genomes]
rs6756184	0.91[EUR][1000 genomes]
rs72909662	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72925431	0.81[AFR][1000 genomes]
rs7568552	0.89[EUR][1000 genomes]
rs9309031	0.89[EUR][1000 genomes]
rs970409	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs997344	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	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
11	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	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
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11124660	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39352400-39355000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:39352400-39355000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:39352400-39355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:39352400-39356800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:39352600-39355000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:39352600-39355200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:39352600-39355200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:39352600-39355200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:39352600-39355200	Weak transcription	Fetal Lung	lung
10	chr2:39352600-39355200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:39352600-39355200	Weak transcription	Fetal Thymus	thymus
12	chr2:39352600-39355600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:39352600-39356400	Weak transcription	Small Intestine	intestine
14	chr2:39352600-39356600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:39352800-39354800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:39352800-39355000	Weak transcription	Primary B cells from cord blood	blood
17	chr2:39352800-39355000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:39352800-39355000	Weak transcription	Primary T cells from cord blood	blood
19	chr2:39352800-39355000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:39352800-39355000	Weak transcription	A549	lung
21	chr2:39352800-39355000	Weak transcription	NHEK	skin
22	chr2:39352800-39355200	Weak transcription	Fetal Intestine Large	intestine
23	chr2:39352800-39362800	Weak transcription	Thymus	Thymus
24	chr2:39352800-39368600	Weak transcription	HMEC	breast
25	chr2:39353000-39355000	Weak transcription	Dnd41	blood
26	chr2:39353000-39355200	Weak transcription	Brain Anterior Caudate	brain
27	chr2:39353000-39355200	Weak transcription	Fetal Intestine Small	intestine
28	chr2:39353000-39355200	Weak transcription	HepG2	liver
29	chr2:39353800-39355400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr2:39354200-39355000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:39354200-39355400	Enhancers	Hela-S3	cervix
32	chr2:39354200-39356600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:39354200-39357800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:39354200-39358400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr2:39354400-39354800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:39354400-39354800	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr2:39354400-39354800	Active TSS	NHLF	lung
38	chr2:39354400-39355400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:39354400-39355400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:39354400-39355600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr2:39354400-39355600	Enhancers	HSMM	muscle
42	chr2:39354400-39356400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr2:39354400-39357600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:39354400-39358600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr2:39354400-39358600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:39354600-39354800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:39354600-39354800	Active TSS	NHDF-Ad	bronchial
48	chr2:39354600-39355000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:39354600-39355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:39354600-39355000	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links