Variant report

Variant	rs379388
Chromosome Location	chr11:17944246-17944247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17938999..17941290-chr11:17942942..17944783,2	MCF-7	breast:
2	chr11:17942744..17945115-chr11:17945670..17947778,2	K562	blood:
3	chr11:17942173..17945463-chr11:17948339..17951076,3	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10766446	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11024435	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11600873	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11603299	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11605018	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12420936	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1401165	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1468291	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1518521	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17793542	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs188397	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2041244	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2097816	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs211095	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs211096	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs211097	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs211098	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs211140	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs211141	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs211144	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs211146	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs211148	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs211149	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs211150	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs211151	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2237909	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2237911	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237913	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2237914	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2237915	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237916	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237917	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2237919	0.80[AFR][1000 genomes]
rs2237920	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2283233	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2283235	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2283237	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2299628	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2670764	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2670765	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4141243	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393297	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs511604	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59573120	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs616099	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66813449	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs728639	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs739916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs757410	0.84[AFR][1000 genomes]
rs7927135	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs916975	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9787863	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs379388	SERGEF	cis	Muscle Skeletal	GTEx
rs379388	SERGEF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17838400-17971600	Weak transcription	Gastric	stomach
2	chr11:17864400-17944800	Weak transcription	Ovary	ovary
3	chr11:17886000-17965200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:17896000-17944600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr11:17896000-17968000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr11:17896400-17968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:17906000-17970200	Weak transcription	Lung	lung
8	chr11:17910600-17947000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:17914600-17965400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:17915800-17966000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:17917000-17944600	Weak transcription	Brain Angular Gyrus	brain
12	chr11:17917000-17947600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:17920600-17976000	Weak transcription	Esophagus	oesophagus
14	chr11:17927600-17944600	Weak transcription	Left Ventricle	heart
15	chr11:17928600-17946200	Weak transcription	Fetal Thymus	thymus
16	chr11:17928600-17970200	Weak transcription	Thymus	Thymus
17	chr11:17929200-17954800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:17933000-17956800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
20	chr11:17935000-17944600	Weak transcription	Fetal Stomach	stomach
21	chr11:17935200-17955000	Strong transcription	Primary T cells from cord blood	blood
22	chr11:17935400-17946400	Weak transcription	Aorta	Aorta
23	chr11:17935600-17944600	Weak transcription	Right Ventricle	heart
24	chr11:17937400-17950600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:17937600-17944600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:17937600-17944600	Weak transcription	Right Atrium	heart
27	chr11:17937600-17949000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:17937600-17977000	Weak transcription	Colon Smooth Muscle	Colon
29	chr11:17937800-17951800	Weak transcription	HSMMtube	muscle
30	chr11:17937800-17965800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:17939000-17950600	Weak transcription	Fetal Intestine Large	intestine
32	chr11:17939200-17946400	Strong transcription	HepG2	liver
33	chr11:17939400-17953400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:17940000-17953000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:17940000-17976400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:17940200-17944400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:17940200-17944600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:17940600-17947800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr11:17940800-17944600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:17941000-17944400	Weak transcription	Primary B cells from cord blood	blood
41	chr11:17941000-17944600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:17941000-17944600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:17941000-17953000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:17941400-17947800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:17942000-17950000	Enhancers	Liver	Liver
46	chr11:17942200-17944400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:17942200-17945000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:17942200-17945400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr11:17942200-17945400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr11:17942200-17945800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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