Variant report

Variant	rs211137
Chromosome Location	chr11:18026461-18026462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18024725..18026485-chr11:18033759..18035414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10488683	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs10766450	0.87[EUR][1000 genomes]
rs12277387	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12292915	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1401166	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs172424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1914710	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2108977	0.87[EUR][1000 genomes]
rs211095	0.83[YRI][hapmap]
rs211096	0.82[YRI][hapmap]
rs211114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211121	0.83[YRI][hapmap]
rs211128	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211139	0.87[ASN][1000 genomes]
rs211140	0.82[YRI][hapmap]
rs211141	0.91[YRI][hapmap]
rs2137777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237919	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2237923	0.95[CEU][hapmap]
rs2283238	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283240	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2299623	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2679116	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs371589	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3741200	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741201	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741202	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3958112	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4757603	0.96[CEU][hapmap]
rs4757607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs484616	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs757410	0.82[EUR][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs211137	SERGEF	cis	Adipose Subcutaneous	GTEx
rs211137	RP1-59M18.2	cis	Muscle Skeletal	GTEx
rs211137	RP1-59M18.2	cis	Adipose Subcutaneous	GTEx
rs211137	SERGEF	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
2	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
5	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
6	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
7	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
10	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:18008400-18026800	Weak transcription	NH-A	brain
15	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
16	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
18	chr11:18009200-18026800	Weak transcription	K562	blood
19	chr11:18009400-18033600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:18010200-18033600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:18010400-18033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:18013800-18029400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:18014200-18028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:18014200-18028600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:18014200-18029000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:18014200-18029200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:18014200-18029800	Strong transcription	Primary T cells from cord blood	blood
28	chr11:18014600-18028000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:18014600-18028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:18014800-18033200	Weak transcription	Stomach Mucosa	stomach
31	chr11:18015200-18033400	Weak transcription	Fetal Heart	heart
32	chr11:18015400-18027400	Weak transcription	Hela-S3	cervix
33	chr11:18016200-18028800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:18016400-18033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:18017000-18027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:18017000-18033600	Weak transcription	NHLF	lung
37	chr11:18018200-18029600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:18019000-18028200	Strong transcription	Adipose Nuclei	Adipose
39	chr11:18019400-18028400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:18019600-18029200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:18020000-18034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr11:18020200-18027600	Strong transcription	Primary B cells from cord blood	blood
43	chr11:18020200-18028200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:18020200-18028200	Strong transcription	Fetal Brain Female	brain
45	chr11:18020200-18028600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:18020200-18028600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr11:18020200-18029200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:18020200-18029400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:18020400-18028400	Strong transcription	Dnd41	blood
50	chr11:18020400-18028600	Strong transcription	Stomach Smooth Muscle	stomach

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