Variant report

Variant	rs10200058
Chromosome Location	chr2:39341253-39341254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39329210..39332058-chr2:39338732..39341739,3	K562	blood:
2	chr2:39340251..39342367-chr2:39346611..39348582,3	MCF-7	breast:
3	chr2:39338748..39341346-chr2:39343772..39345520,2	MCF-7	breast:
4	chr2:38977093..38979602-chr2:39339599..39342349,3	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10165968	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10177250	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10184015	0.85[EUR][1000 genomes]
rs10190377	0.90[EUR][1000 genomes]
rs10206751	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11124660	0.83[EUR][1000 genomes]
rs12620003	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620071	0.82[EUR][1000 genomes]
rs12622969	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031871	0.86[EUR][1000 genomes]
rs13033392	0.90[EUR][1000 genomes]
rs1377860	0.82[EUR][1000 genomes]
rs1377861	0.82[EUR][1000 genomes]
rs1377864	0.85[EUR][1000 genomes]
rs1454227	0.89[EUR][1000 genomes]
rs1470914	0.89[EUR][1000 genomes]
rs2060988	0.80[EUR][1000 genomes]
rs2060989	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs212322	0.84[ASN][1000 genomes]
rs2123882	0.87[EUR][1000 genomes]
rs2168043	0.85[ASN][1000 genomes]
rs2373497	0.81[EUR][1000 genomes]
rs2924714	0.82[EUR][1000 genomes]
rs2969763	0.82[EUR][1000 genomes]
rs297120	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs297121	0.82[EUR][1000 genomes]
rs297124	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs297125	0.82[EUR][1000 genomes]
rs297127	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs297128	0.82[EUR][1000 genomes]
rs297129	0.82[EUR][1000 genomes]
rs297130	0.82[EUR][1000 genomes]
rs297131	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297132	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297133	0.82[EUR][1000 genomes]
rs297134	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297135	0.82[EUR][1000 genomes]
rs297136	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297137	0.82[EUR][1000 genomes]
rs297139	0.82[EUR][1000 genomes]
rs297140	0.82[EUR][1000 genomes]
rs297141	0.82[EUR][1000 genomes]
rs297142	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297143	0.82[EUR][1000 genomes]
rs297144	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297145	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297147	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs297148	0.82[EUR][1000 genomes]
rs297149	0.82[EUR][1000 genomes]
rs297150	0.82[EUR][1000 genomes]
rs297151	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297152	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs297153	0.82[EUR][1000 genomes]
rs297155	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297156	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297157	0.82[EUR][1000 genomes]
rs297158	0.83[EUR][1000 genomes]
rs297159	0.82[EUR][1000 genomes]
rs297161	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs297162	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs366840	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs378698	0.82[EUR][1000 genomes]
rs3796038	0.89[EUR][1000 genomes]
rs388958	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670905	0.82[EUR][1000 genomes]
rs57378308	0.83[EUR][1000 genomes]
rs59732351	0.83[EUR][1000 genomes]
rs61405040	0.82[EUR][1000 genomes]
rs6419600	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6544191	0.82[EUR][1000 genomes]
rs6544197	0.82[EUR][1000 genomes]
rs6726833	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6758330	0.83[EUR][1000 genomes]
rs72909662	0.83[EUR][1000 genomes]
rs970409	0.82[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
rs10200058	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
2	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:39321000-39344600	Weak transcription	Gastric	stomach
4	chr2:39322400-39345200	Weak transcription	Osteobl	bone
5	chr2:39322600-39344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:39322800-39345200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:39323000-39344800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:39327000-39344600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39328000-39346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:39328200-39344600	Weak transcription	Hela-S3	cervix
11	chr2:39330000-39346800	Weak transcription	Spleen	Spleen
12	chr2:39334200-39345000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:39334600-39342600	Weak transcription	Fetal Lung	lung
14	chr2:39334600-39344400	Weak transcription	Small Intestine	intestine
15	chr2:39334600-39344600	Weak transcription	NHLF	lung
16	chr2:39334600-39345200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:39334600-39345400	Weak transcription	NH-A	brain
18	chr2:39334600-39346000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:39334600-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:39334800-39343200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:39334800-39345200	Weak transcription	HSMMtube	muscle
22	chr2:39334800-39345400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:39334800-39345600	Weak transcription	HSMM	muscle
24	chr2:39335000-39344800	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:39335200-39341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:39335200-39344400	Weak transcription	Liver	Liver
27	chr2:39335200-39344600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:39335200-39344800	Weak transcription	Ovary	ovary
29	chr2:39335200-39345000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:39335200-39345200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:39335200-39345800	Weak transcription	Brain Substantia Nigra	brain
32	chr2:39335400-39342800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:39335400-39342800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:39335400-39342800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:39335400-39344400	Weak transcription	Fetal Heart	heart
36	chr2:39335400-39344600	Weak transcription	NHEK	skin
37	chr2:39335400-39345000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:39335400-39345400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:39335600-39344600	Weak transcription	Fetal Brain Female	brain
40	chr2:39335600-39345200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:39335600-39345200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:39335600-39345200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:39335800-39344400	Weak transcription	K562	blood
44	chr2:39336000-39345400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:39336200-39343200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:39337000-39345200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:39337200-39342800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:39337200-39344800	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:39337400-39343800	Weak transcription	Fetal Brain Male	brain
50	chr2:39337400-39345400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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