Variant report

Variant	rs10170424
Chromosome Location	chr2:39640739-39640740
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39635451..39641229-chr2:39641645..39645299,6	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10153665	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10169391	0.87[AFR][1000 genomes]
rs10170604	0.90[AFR][1000 genomes]
rs10170617	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10172736	0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs10173556	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10175038	0.85[EUR][1000 genomes]
rs10175333	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs10181650	0.95[AFR][1000 genomes]
rs10190069	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10193636	0.86[CHB][hapmap]
rs10195629	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035232	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865149	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10865150	1.00[ASW][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes]
rs10865152	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11124668	0.85[EUR][1000 genomes]
rs11124673	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11124676	0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124677	0.82[AFR][1000 genomes]
rs11124679	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11124681	0.91[AFR][1000 genomes]
rs1125839	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11688728	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1211996	0.87[EUR][1000 genomes]
rs12622941	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712641	0.90[AFR][1000 genomes]
rs13028561	0.95[AFR][1000 genomes]
rs1468902	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1474424	0.91[ASW][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs1477164	0.89[AFR][1000 genomes]
rs17023837	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1861735	0.88[EUR][1000 genomes]
rs1922827	0.91[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2005892	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2056654	0.90[AFR][1000 genomes]
rs2178762	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2193422	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2373534	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2373535	0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2373536	0.94[YRI][hapmap];0.95[AFR][1000 genomes]
rs2542008	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2888594	0.90[EUR][1000 genomes]
rs2888598	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755177	0.88[EUR][1000 genomes]
rs3755178	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770670	0.88[EUR][1000 genomes]
rs3770675	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770678	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3887311	0.81[AMR][1000 genomes]
rs4670934	1.00[ASW][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs4670935	0.94[YRI][hapmap];0.93[AFR][1000 genomes]
rs4670936	0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs6419603	0.89[AFR][1000 genomes]
rs6544213	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544220	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6544222	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544223	1.00[ASW][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.89[AFR][1000 genomes]
rs6544224	0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6544228	0.90[AFR][1000 genomes]
rs6712274	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6712921	0.83[EUR][1000 genomes]
rs6717792	0.85[AFR][1000 genomes]
rs6718134	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6724393	0.95[AFR][1000 genomes]
rs6725938	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6730902	0.90[AFR][1000 genomes]
rs6732611	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6736700	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741019	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742170	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743041	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6753323	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756183	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6759495	0.90[AFR][1000 genomes]
rs6760382	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7574250	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7578136	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7579414	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7582160	1.00[ASW][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs7591102	0.87[AFR][1000 genomes]
rs7595041	0.95[AFR][1000 genomes]
rs759589	0.90[EUR][1000 genomes]
rs7600014	0.83[ASW][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs7600046	0.88[EUR][1000 genomes]
rs7601700	1.00[ASW][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7603337	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7603392	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7608153	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	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
2	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
3	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
rs10170424	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain
4	chr2:39622800-39643400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:39632400-39643400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39632600-39641400	Enhancers	Fetal Heart	heart
7	chr2:39633000-39641200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:39633000-39644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:39634400-39641000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:39634600-39643800	Weak transcription	Fetal Brain Female	brain
11	chr2:39635000-39644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:39635400-39643200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:39635600-39643400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:39636200-39642400	Weak transcription	Primary B cells from cord blood	blood
15	chr2:39636600-39651400	Weak transcription	Fetal Thymus	thymus
16	chr2:39636800-39641000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr2:39636800-39641600	Enhancers	Colon Smooth Muscle	Colon
18	chr2:39637200-39647000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:39637600-39643800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:39637600-39651400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:39638200-39641000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:39638200-39641000	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:39638200-39641400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:39638200-39641400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr2:39638200-39641400	Enhancers	Brain Anterior Caudate	brain
27	chr2:39638400-39640800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:39638400-39641200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:39638600-39641400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:39638800-39640800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:39638800-39640800	Enhancers	NH-A	brain
32	chr2:39638800-39641200	Enhancers	HSMM	muscle
33	chr2:39638800-39644400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:39638800-39652400	Weak transcription	Hela-S3	cervix
35	chr2:39639000-39641000	Enhancers	Osteobl	bone
36	chr2:39639000-39641600	Enhancers	NHDF-Ad	bronchial
37	chr2:39639000-39649000	Weak transcription	Primary T cells from cord blood	blood
38	chr2:39639200-39641000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:39639200-39641200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr2:39639200-39643400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:39639200-39644800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
43	chr2:39639400-39640800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:39639400-39642000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:39639400-39642400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:39639400-39643800	Weak transcription	Stomach Mucosa	stomach
47	chr2:39639400-39644000	Weak transcription	Fetal Kidney	kidney
48	chr2:39639600-39643400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:39639600-39646800	Weak transcription	Fetal Lung	lung
50	chr2:39639600-39657200	Weak transcription	HMEC	breast

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