Variant report

Variant	rs2041244
Chromosome Location	chr11:18012337-18012338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10741734	0.82[EUR][1000 genomes]
rs10766446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10832872	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11024435	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024446	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11600873	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11603299	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11605018	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12292490	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12420936	0.80[EUR][1000 genomes]
rs1401163	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401164	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1401165	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468291	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1518521	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1518522	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1607395	0.81[EUR][1000 genomes]
rs169806	0.86[AFR][1000 genomes]
rs17793542	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1799913	0.81[EUR][1000 genomes]
rs1800532	0.81[EUR][1000 genomes]
rs188397	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097816	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211095	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211096	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211097	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211098	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211140	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211141	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211144	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211146	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211148	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211149	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211150	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs211151	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237907	0.81[EUR][1000 genomes]
rs2237908	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237909	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237911	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237913	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237914	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237915	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237916	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2237917	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237920	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2283233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283235	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283237	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299625	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299628	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2670764	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2670765	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379388	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4141243	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4393297	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs511604	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59573120	0.80[EUR][1000 genomes]
rs616099	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654734	0.86[AFR][1000 genomes]
rs66813449	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs685657	0.86[AFR][1000 genomes]
rs72862028	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs728639	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs739916	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7927135	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933505	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs887242	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs916975	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9787863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2041244	SERGEF	Cis_1M	lymphoblastoid	RTeQTL
rs2041244	SERGEF	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 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	chr11:17966400-18014400	Weak transcription	Fetal Thymus	thymus
6	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:17975000-18020200	Weak transcription	A549	lung
8	chr11:17978200-18016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:17979800-18016400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
11	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
12	chr11:17989400-18023400	Weak transcription	Gastric	stomach
13	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
14	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
17	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:18000800-18014600	Weak transcription	Spleen	Spleen
19	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:18003600-18012400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr11:18006800-18021000	Weak transcription	Placenta	Placenta
22	chr11:18007000-18012600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr11:18007000-18017800	Strong transcription	Dnd41	blood
24	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:18007600-18014200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:18007600-18016600	Weak transcription	Aorta	Aorta
27	chr11:18007800-18021000	Weak transcription	Psoas Muscle	Psoas
28	chr11:18008200-18014800	Weak transcription	Fetal Heart	heart
29	chr11:18008200-18016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:18008200-18025800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:18008400-18013800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:18008400-18015000	Weak transcription	Lung	lung
34	chr11:18008400-18016200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:18008400-18023800	Weak transcription	Fetal Lung	lung
36	chr11:18008400-18026800	Weak transcription	NH-A	brain
37	chr11:18008600-18012600	Strong transcription	Ovary	ovary
38	chr11:18008600-18016400	Weak transcription	NHLF	lung
39	chr11:18008600-18022600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
41	chr11:18008800-18014400	Weak transcription	HSMMtube	muscle
42	chr11:18008800-18020800	Weak transcription	Fetal Kidney	kidney
43	chr11:18008800-18025800	Weak transcription	NHEK	skin
44	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
46	chr11:18009000-18016000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:18009000-18020400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:18009200-18017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:18009200-18020400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:18009200-18021600	Weak transcription	Fetal Intestine Small	intestine

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