Variant report

Variant	rs10173556
Chromosome Location	chr2:39604093-39604094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
2	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
3	chr2:39596692..39599194-chr2:39603552..39605779,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10153665	0.92[EUR][1000 genomes]
rs10169391	0.81[AFR][1000 genomes]
rs10170424	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10170604	0.90[AFR][1000 genomes]
rs10170617	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10172736	0.89[EUR][1000 genomes]
rs10175038	0.89[EUR][1000 genomes]
rs10175333	0.85[AFR][1000 genomes]
rs10181650	0.86[AFR][1000 genomes]
rs10190069	0.82[EUR][1000 genomes]
rs10195629	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035232	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865149	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10865150	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10865152	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11124668	0.89[EUR][1000 genomes]
rs11124673	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11124676	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11124677	0.84[AFR][1000 genomes]
rs11124679	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124681	0.83[AFR][1000 genomes]
rs1125839	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11688728	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1211996	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12622941	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712636	0.83[EUR][1000 genomes]
rs12712641	0.90[AFR][1000 genomes]
rs13028561	0.86[AFR][1000 genomes]
rs1468902	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474424	0.89[AFR][1000 genomes]
rs1477164	0.89[AFR][1000 genomes]
rs17023837	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1861735	0.92[EUR][1000 genomes]
rs1922827	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2005892	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2056654	0.85[AFR][1000 genomes]
rs2178760	0.82[EUR][1000 genomes]
rs2178762	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2193422	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2373534	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2373535	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2373536	0.86[AFR][1000 genomes]
rs2542008	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888594	0.90[EUR][1000 genomes]
rs2888598	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755177	0.92[EUR][1000 genomes]
rs3755178	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770670	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3770675	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770678	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670934	0.85[AFR][1000 genomes]
rs4670935	0.85[AFR][1000 genomes]
rs4670936	0.84[AFR][1000 genomes]
rs6419603	0.89[AFR][1000 genomes]
rs6544213	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544220	0.87[EUR][1000 genomes]
rs6544222	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6544223	0.89[AFR][1000 genomes]
rs6544224	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6544228	0.85[AFR][1000 genomes]
rs6712274	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6712921	0.91[EUR][1000 genomes]
rs6717792	0.80[AFR][1000 genomes]
rs6718134	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6724393	0.86[AFR][1000 genomes]
rs6725938	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6730902	0.85[AFR][1000 genomes]
rs6732611	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736700	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741019	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6742170	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743041	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6753323	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756183	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6759495	0.85[AFR][1000 genomes]
rs6760382	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7568561	0.86[AMR][1000 genomes]
rs7574250	0.81[AMR][1000 genomes]
rs7578136	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7579414	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7582160	0.92[AFR][1000 genomes]
rs7595041	0.86[AFR][1000 genomes]
rs759589	0.94[EUR][1000 genomes]
rs7600014	0.92[EUR][1000 genomes]
rs7600046	0.92[EUR][1000 genomes]
rs7601700	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7603337	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7603392	0.85[AFR][1000 genomes]
rs7604047	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7608153	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
rs10173556	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
2	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
3	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39588000-39607800	Weak transcription	Ovary	ovary
6	chr2:39588000-39608800	Weak transcription	Lung	lung
7	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
9	chr2:39590000-39604800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:39590200-39604800	Weak transcription	HSMMtube	muscle
11	chr2:39591800-39604600	Weak transcription	NH-A	brain
12	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39592000-39606800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:39592400-39604600	Weak transcription	Fetal Heart	heart
15	chr2:39592600-39607000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
18	chr2:39595800-39604600	Weak transcription	Psoas Muscle	Psoas
19	chr2:39595800-39606800	Weak transcription	HUVEC	blood vessel
20	chr2:39595800-39607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:39596200-39605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:39596400-39604600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:39596400-39605000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:39596400-39606800	Weak transcription	Fetal Brain Male	brain
25	chr2:39596800-39605600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:39597200-39607800	Weak transcription	Small Intestine	intestine
27	chr2:39597600-39604400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:39597600-39604800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:39597600-39605600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:39597600-39606200	Weak transcription	Brain Anterior Caudate	brain
31	chr2:39597600-39606200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:39598600-39606400	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:39598800-39604600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:39600000-39606400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:39600600-39606800	Weak transcription	Fetal Kidney	kidney
36	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
37	chr2:39600800-39606200	Weak transcription	Brain Substantia Nigra	brain
38	chr2:39601000-39604400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:39601000-39604600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:39601000-39604800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:39601000-39605000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:39601000-39606800	Weak transcription	NHEK	skin
43	chr2:39601200-39604600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:39601200-39606200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:39601400-39604600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:39601400-39607000	Weak transcription	Fetal Brain Female	brain
47	chr2:39601600-39609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr2:39601800-39606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:39602400-39604600	Weak transcription	Fetal Intestine Small	intestine
50	chr2:39602800-39604600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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