Variant report

Variant	rs11164942
Chromosome Location	chr1:93975436-93975437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1055654	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10874786	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10874790	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164936	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164938	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164943	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12042552	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12123339	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12135266	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12742850	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812668	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs237438	0.80[ASN][1000 genomes]
rs237439	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2624436	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2624439	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3767967	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847245	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847428	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4847429	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847431	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546702	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7551016	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8179368	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011853	chr1:93966450-94039005	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv946083	chr1:93975114-93983709	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11164942	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93958000-93997200	Weak transcription	HSMMtube	muscle
2	chr1:93958800-93991800	Weak transcription	Gastric	stomach
3	chr1:93961000-93988400	Weak transcription	HUVEC	blood vessel
4	chr1:93962600-93984200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:93964600-93990200	Weak transcription	HSMM	muscle
6	chr1:93964600-94015200	Weak transcription	Fetal Brain Male	brain
7	chr1:93965000-94013200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:93965000-94017400	Weak transcription	Stomach Mucosa	stomach
9	chr1:93965200-93984600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:93965200-93984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:93965400-93983600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:93967400-93984200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:93968600-93976800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:93968600-93984400	Weak transcription	NHEK	skin
15	chr1:93971800-93975600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr1:93971800-93975600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr1:93972200-93993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:93972400-93977000	Weak transcription	Lung	lung
19	chr1:93973200-94016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:93973400-94032000	Weak transcription	Esophagus	oesophagus
21	chr1:93974000-93985000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:93974400-93975600	ZNF genes & repeats	Fetal Intestine Large	intestine
23	chr1:93974800-93975600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:93974800-93975600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:93975000-93975600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:93975000-93976000	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:93975000-93978000	Weak transcription	K562	blood
28	chr1:93975000-93981800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:93975000-93986800	Weak transcription	Pancreas	Pancrea
30	chr1:93975000-93988200	Weak transcription	Fetal Kidney	kidney
31	chr1:93975000-93996800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:93975200-93984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:93975200-93986200	Weak transcription	HepG2	liver
34	chr1:93975200-93986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:93975200-93988400	Weak transcription	Dnd41	blood
36	chr1:93975200-93996800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:93975200-93997000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:93975400-93976200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:93975400-93978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:93975400-93981800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:93975400-93985200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:93975400-93986000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:93975400-93986200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:93975400-93986600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:93975400-93986600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:93975400-93986800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:93975400-93987800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:93975400-93991800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:93975400-93995200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:93975400-93996000	Weak transcription	Fetal Lung	lung

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