Variant report

Variant	rs211128
Chromosome Location	chr11:18015355-18015356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18013613..18016047-chr11:18016241..18018614,3	K562	blood:
2	chr11:18013568..18016521-chr11:18123869..18126063,2	K562	blood:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10488683	0.96[CEU][hapmap]
rs10766450	0.80[EUR][1000 genomes]
rs11024429	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12277387	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12292915	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1401166	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs172424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1914710	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108977	0.80[EUR][1000 genomes]
rs211095	0.84[YRI][hapmap]
rs211096	0.83[YRI][hapmap]
rs211114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs211131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs211135	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211136	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211137	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]
rs211140	0.83[YRI][hapmap]
rs211148	0.96[YRI][hapmap]
rs2137777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237913	0.96[YRI][hapmap]
rs2237914	0.85[YRI][hapmap]
rs2237919	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237923	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2283238	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283240	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2299623	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299628	1.00[YRI][hapmap]
rs2670765	0.91[YRI][hapmap]
rs2679116	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34832793	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371589	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3958112	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4757603	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4757607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484616	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59881258	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs757410	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs916975	0.85[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs211128	SERGEF	cis	Muscle Skeletal	GTEx
rs211128	SERGEF	cis	Adipose Subcutaneous	GTEx
rs211128	RP1-59M18.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 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	chr11:17961000-18016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:17975000-18020200	Weak transcription	A549	lung
7	chr11:17978200-18016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:17979800-18016400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
10	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
11	chr11:17989400-18023400	Weak transcription	Gastric	stomach
12	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
13	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
16	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:18006800-18021000	Weak transcription	Placenta	Placenta
19	chr11:18007000-18017800	Strong transcription	Dnd41	blood
20	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:18007600-18016600	Weak transcription	Aorta	Aorta
22	chr11:18007800-18021000	Weak transcription	Psoas Muscle	Psoas
23	chr11:18008200-18016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:18008200-18025800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:18008400-18016200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:18008400-18023800	Weak transcription	Fetal Lung	lung
28	chr11:18008400-18026800	Weak transcription	NH-A	brain
29	chr11:18008600-18016400	Weak transcription	NHLF	lung
30	chr11:18008600-18022600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
32	chr11:18008800-18020800	Weak transcription	Fetal Kidney	kidney
33	chr11:18008800-18025800	Weak transcription	NHEK	skin
34	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
36	chr11:18009000-18016000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:18009000-18020400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:18009200-18017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:18009200-18020400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:18009200-18021600	Weak transcription	Fetal Intestine Small	intestine
41	chr11:18009200-18026200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr11:18009200-18026800	Weak transcription	K562	blood
43	chr11:18009400-18020600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:18009400-18033600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:18009600-18020600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:18009600-18021200	Weak transcription	Osteobl	bone
47	chr11:18009800-18016200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:18009800-18016600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:18010000-18016800	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:18010200-18015400	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links