Variant report

Variant	rs2542008
Chromosome Location	chr2:39594111-39594112
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	chr2:39594087..39595987-chr2:39607916..39609547,2	MCF-7	breast:
2	chr2:39592431..39595037-chr2:39606994..39609633,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10153665	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10170424	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10170617	0.92[EUR][1000 genomes]
rs10172736	0.88[EUR][1000 genomes]
rs10173556	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10175038	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10190069	0.89[EUR][1000 genomes]
rs10195629	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1035232	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865149	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865150	0.96[EUR][1000 genomes]
rs10865152	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124668	0.88[EUR][1000 genomes]
rs11124673	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11124676	0.84[EUR][1000 genomes]
rs11124679	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1125839	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11688728	0.82[EUR][1000 genomes]
rs1211996	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12622941	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712636	0.86[EUR][1000 genomes]
rs1468902	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17023837	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1861735	0.92[EUR][1000 genomes]
rs1922827	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2005892	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178760	0.81[ASN][1000 genomes]
rs2178762	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193422	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2373534	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373535	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888594	0.94[EUR][1000 genomes]
rs2888598	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3755177	0.92[EUR][1000 genomes]
rs3755178	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770670	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770675	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770678	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544213	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544220	0.84[EUR][1000 genomes]
rs6544222	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544224	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6712274	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6712921	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6718134	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6725938	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6732611	0.87[EUR][1000 genomes]
rs6736700	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6741019	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6742170	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6743041	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6753323	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756183	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6760382	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7568561	0.80[ASN][1000 genomes]
rs7574250	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7578136	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7579414	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs759589	0.94[EUR][1000 genomes]
rs7600014	0.92[EUR][1000 genomes]
rs7600046	0.92[EUR][1000 genomes]
rs7601700	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7603337	0.94[EUR][1000 genomes]
rs7604047	0.82[EUR][1000 genomes]
rs7608153	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
rs2542008	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39572200-39597600	Weak transcription	Osteobl	bone
2	chr2:39584400-39598400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
4	chr2:39587000-39596800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:39587000-39597000	Weak transcription	NHLF	lung
6	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
7	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39587800-39594400	Weak transcription	Stomach Mucosa	stomach
9	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:39588000-39595400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:39588000-39607800	Weak transcription	Ovary	ovary
12	chr2:39588000-39608800	Weak transcription	Lung	lung
13	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
15	chr2:39588200-39599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:39588200-39602800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:39588200-39603000	Weak transcription	Adipose Nuclei	Adipose
18	chr2:39588400-39596800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:39588400-39603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:39588600-39599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:39589400-39594800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:39589600-39595600	Weak transcription	Primary T cells from cord blood	blood
23	chr2:39590000-39597000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:39590000-39604800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:39590200-39594200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:39590200-39597000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:39590200-39597200	Weak transcription	NHDF-Ad	bronchial
28	chr2:39590200-39597400	Weak transcription	NHEK	skin
29	chr2:39590200-39598200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:39590200-39598400	Weak transcription	Fetal Lung	lung
31	chr2:39590200-39599800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:39590200-39602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:39590200-39602800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:39590200-39604800	Weak transcription	HSMMtube	muscle
35	chr2:39590400-39598200	Weak transcription	Primary B cells from cord blood	blood
36	chr2:39590400-39599800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:39590400-39600400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:39590400-39602400	Weak transcription	Liver	Liver
39	chr2:39590600-39598200	Weak transcription	Fetal Intestine Large	intestine
40	chr2:39590600-39598200	Weak transcription	HSMM	muscle
41	chr2:39590600-39598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39590600-39598600	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:39590600-39601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:39590600-39601200	Weak transcription	Fetal Stomach	stomach
45	chr2:39590600-39602200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:39590800-39595000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:39590800-39595400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:39591000-39602000	Weak transcription	Fetal Thymus	thymus
49	chr2:39591800-39595000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:39591800-39602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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