Variant report

Variant	rs11024446
Chromosome Location	chr11:18026663-18026664
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	chr11:17228083..17230231-chr11:18026623..18029632,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070081	Chromatin interaction
ENSG00000011405	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10741734	0.90[EUR][1000 genomes]
rs10766446	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832872	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10832874	0.86[EUR][1000 genomes]
rs11600873	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11605018	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12292490	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1401163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1401165	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1468291	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1518521	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1518522	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1607395	0.89[EUR][1000 genomes]
rs169806	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17793542	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1799913	0.89[EUR][1000 genomes]
rs1800532	0.89[EUR][1000 genomes]
rs188397	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2041244	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2056246	0.88[EUR][1000 genomes]
rs2071532	0.85[EUR][1000 genomes]
rs2097816	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs211095	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211096	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211097	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211098	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211106	0.83[EUR][1000 genomes]
rs211107	0.87[EUR][1000 genomes]
rs211108	0.87[EUR][1000 genomes]
rs211140	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211141	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs211144	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211146	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs211148	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211149	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211150	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211151	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237907	0.89[EUR][1000 genomes]
rs2237908	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237909	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237911	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237913	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237914	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237915	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237916	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237917	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2237920	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2283233	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2283235	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2283237	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299628	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2670764	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2670765	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs508924	0.87[EUR][1000 genomes]
rs511604	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs517005	0.83[EUR][1000 genomes]
rs544437	0.81[EUR][1000 genomes]
rs546383	0.84[EUR][1000 genomes]
rs572940	0.82[EUR][1000 genomes]
rs593839	0.86[EUR][1000 genomes]
rs616099	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652458	0.87[EUR][1000 genomes]
rs654734	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs66813449	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684302	0.87[EUR][1000 genomes]
rs685657	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72862028	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728639	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7927135	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7933505	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs887242	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs916975	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9787863	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11024446	SERGEF	cis	Muscle Skeletal	GTEx
rs11024446	SERGEF	Cis_1M	lymphoblastoid	RTeQTL

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	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
4	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
5	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
6	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
9	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:18008400-18026800	Weak transcription	NH-A	brain
14	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
15	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
17	chr11:18009200-18026800	Weak transcription	K562	blood
18	chr11:18009400-18033600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:18010200-18033600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:18010400-18033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:18013800-18029400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:18014200-18028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:18014200-18028600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:18014200-18029000	Strong transcription	Primary B cells from peripheral blood	blood
25	chr11:18014200-18029200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr11:18014200-18029800	Strong transcription	Primary T cells from cord blood	blood
27	chr11:18014600-18028000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr11:18014600-18028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:18014800-18033200	Weak transcription	Stomach Mucosa	stomach
30	chr11:18015200-18033400	Weak transcription	Fetal Heart	heart
31	chr11:18015400-18027400	Weak transcription	Hela-S3	cervix
32	chr11:18016200-18028800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:18016400-18033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:18017000-18027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:18017000-18033600	Weak transcription	NHLF	lung
36	chr11:18018200-18029600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:18019000-18028200	Strong transcription	Adipose Nuclei	Adipose
38	chr11:18019400-18028400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:18019600-18029200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:18020000-18034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:18020200-18027600	Strong transcription	Primary B cells from cord blood	blood
42	chr11:18020200-18028200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:18020200-18028200	Strong transcription	Fetal Brain Female	brain
44	chr11:18020200-18028600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:18020200-18028600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr11:18020200-18029200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:18020200-18029400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:18020400-18028400	Strong transcription	Dnd41	blood
49	chr11:18020400-18028600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:18020400-18028800	Strong transcription	Primary monocytes fromperipheralblood	blood

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