Variant report

Variant	rs2237913
Chromosome Location	chr11:17977042-17977043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10741734	1.00[CEU][hapmap]
rs10766446	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024435	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024446	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11600873	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603299	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605018	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12292490	1.00[CEU][hapmap];0.96[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12420936	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401163	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1401164	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1401165	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401166	0.95[CEU][hapmap]
rs1468291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1518521	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607395	0.96[CEU][hapmap]
rs169806	0.96[CEU][hapmap]
rs17793542	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800532	0.96[CEU][hapmap]
rs188397	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041244	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056246	0.92[CEU][hapmap]
rs2097816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211096	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211097	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211098	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211107	0.96[CEU][hapmap]
rs211114	0.82[YRI][hapmap]
rs211115	0.82[YRI][hapmap]
rs211128	0.96[YRI][hapmap]
rs211140	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211144	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211148	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211149	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211150	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211151	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191091	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2237908	0.81[EUR][1000 genomes]
rs2237909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237911	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237920	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283233	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283235	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283237	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299625	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670764	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670765	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs379388	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4141243	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4393297	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4757607	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs484616	0.82[YRI][hapmap]
rs508924	0.96[CEU][hapmap]
rs511604	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517005	0.92[CEU][hapmap]
rs546383	0.96[CEU][hapmap]
rs59573120	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616099	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66813449	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs684302	0.92[CEU][hapmap]
rs685657	0.91[CEU][hapmap]
rs72862028	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs728639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739916	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7927135	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933505	0.96[CEU][hapmap]
rs887242	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs916975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787863	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2237913	SERGEF	cis	normal skin	skin_eQTL
rs2237913	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs2237913	SERGEF	cis	Muscle Skeletal	GTEx

Chromatin state (count:112 , 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	chr11:17943800-17992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:17945400-18010000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:17948800-17981400	Weak transcription	Fetal Brain Male	brain
7	chr11:17955400-17978200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:17957200-17994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:17959200-18007600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr11:17961000-18016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:17965400-17994400	Weak transcription	NH-A	brain
12	chr11:17966000-17992600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:17966400-17983400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:17966400-17984400	Strong transcription	Primary T cells from cord blood	blood
15	chr11:17966400-18014400	Weak transcription	Fetal Thymus	thymus
16	chr11:17966600-17994200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:17966800-17977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:17966800-17984800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:17967400-17984400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:17967600-17984200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr11:17967600-17984400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr11:17967800-17983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:17968200-17986200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:17968600-17984400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:17968600-18007000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:17969200-17984400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:17969400-17979400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr11:17970600-17979800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:17971400-17984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:17971600-17994200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr11:17972200-17981600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:17972400-17977600	Strong transcription	Fetal Intestine Large	intestine
34	chr11:17972600-17978400	Weak transcription	Fetal Intestine Small	intestine
35	chr11:17972800-17984200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:17972800-17994200	Weak transcription	NHEK	skin
37	chr11:17973000-17978800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:17973800-18008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:17974000-17984400	Strong transcription	Dnd41	blood
40	chr11:17974200-17977200	Enhancers	Psoas Muscle	Psoas
41	chr11:17974200-17984000	Strong transcription	Adipose Nuclei	Adipose
42	chr11:17974200-17985800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:17974200-18007000	Weak transcription	Fetal Lung	lung
44	chr11:17974400-17978400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:17974400-17978800	Strong transcription	Ovary	ovary
46	chr11:17974400-18001200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr11:17974400-18007200	Weak transcription	Stomach Mucosa	stomach
48	chr11:17974400-18007400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:17974600-17979800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr11:17974600-17984400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links