Variant report

Variant	rs1125839
Chromosome Location	chr2:39564620-39564621
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39548716..39551632-chr2:39563065..39564786,2	MCF-7	breast:
2	chr2:39564092..39565886-chr2:39568968..39572461,3	K562	blood:

Variant related genes	Relation type
ENSG00000273035	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10153665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10170424	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10170617	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10172736	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10173556	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10174268	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10175038	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10175333	0.94[YRI][hapmap]
rs10190069	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10195629	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035232	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865149	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865150	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865152	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124668	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11124673	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11124676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124677	0.83[AFR][1000 genomes]
rs11124679	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11688728	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1211996	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13005378	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs13028683	0.81[JPT][hapmap]
rs1468902	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1474424	0.94[YRI][hapmap]
rs1477164	0.86[YRI][hapmap]
rs1548170	0.86[CHB][hapmap]
rs17023372	0.86[CHB][hapmap]
rs17023837	0.87[EUR][1000 genomes]
rs1861735	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1922827	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2005892	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178762	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2193422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2373527	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2373534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2373535	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs2373536	0.94[YRI][hapmap]
rs2542008	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2665157	0.88[YRI][hapmap]
rs2708222	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2708223	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2888594	0.90[EUR][1000 genomes]
rs2888598	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3755177	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3755178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770670	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3770675	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770678	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4670918	0.86[CHB][hapmap]
rs4670934	0.88[YRI][hapmap]
rs4670935	0.94[YRI][hapmap]
rs4670936	0.84[YRI][hapmap]
rs6544210	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6544213	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6544220	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544222	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6544223	0.88[YRI][hapmap]
rs6544224	0.87[CEU][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706711	0.86[CHB][hapmap]
rs6710989	0.88[YRI][hapmap]
rs6712274	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6712921	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6718134	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6725938	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732611	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6736700	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741019	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6742170	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6753323	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6760382	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7562981	0.86[CHB][hapmap]
rs7566123	0.86[CHB][hapmap]
rs7569834	0.86[CHB][hapmap]
rs7574250	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7575216	0.86[CHB][hapmap]
rs7578136	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579414	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7582160	1.00[YRI][hapmap]
rs759589	0.94[EUR][1000 genomes]
rs7600014	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7600046	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7601700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7603337	0.90[EUR][1000 genomes]
rs7603392	0.94[YRI][hapmap]
rs7604047	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7608153	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	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
19	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
20	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	esv2762497	chr2:39540753-39566724	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1125839	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39481000-39580200	Weak transcription	NHEK	skin
2	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
5	chr2:39517600-39566400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:39519800-39583000	Weak transcription	Brain Angular Gyrus	brain
7	chr2:39520000-39586200	Weak transcription	Fetal Kidney	kidney
8	chr2:39520400-39565800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:39524000-39583600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39528800-39581800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:39534000-39586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39538800-39572000	Weak transcription	Small Intestine	intestine
13	chr2:39539000-39583800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:39539000-39586400	Weak transcription	Pancreas	Pancrea
15	chr2:39541000-39586400	Weak transcription	Lung	lung
16	chr2:39541400-39582200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:39542200-39565600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:39543000-39569400	Weak transcription	HUVEC	blood vessel
19	chr2:39545400-39585800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:39553800-39569000	Weak transcription	HMEC	breast
21	chr2:39554000-39571000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:39554600-39586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:39555400-39566600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:39555400-39581200	Weak transcription	Fetal Muscle Leg	muscle
25	chr2:39555400-39581200	Weak transcription	Fetal Stomach	stomach
26	chr2:39555600-39581400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:39555600-39582200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39556000-39581600	Weak transcription	Placenta	Placenta
29	chr2:39556200-39582400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:39556400-39585000	Weak transcription	Primary B cells from cord blood	blood
31	chr2:39556600-39571200	Weak transcription	A549	lung
32	chr2:39556800-39582200	Weak transcription	Left Ventricle	heart
33	chr2:39557000-39582400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:39557000-39586800	Weak transcription	Aorta	Aorta
35	chr2:39557200-39566200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:39557200-39580800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:39557200-39582600	Weak transcription	Primary T cells from cord blood	blood
38	chr2:39557200-39586000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:39557600-39581600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:39557800-39581600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:39558000-39565800	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:39558400-39583800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:39558600-39584000	Weak transcription	Ovary	ovary
44	chr2:39558800-39566200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr2:39558800-39576800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:39558800-39578200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:39558800-39586600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:39559000-39571000	Weak transcription	NH-A	brain
49	chr2:39559000-39581800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:39559000-39586400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links