Variant report

Variant	rs3850350
Chromosome Location	chr2:54898633-54898634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10170355	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10176359	0.88[CHB][hapmap]
rs10176445	0.88[CHB][hapmap]
rs10182836	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10183043	0.81[EUR][1000 genomes]
rs10183867	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10184128	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10188185	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10193692	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10205410	0.84[CHB][hapmap]
rs10206143	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs10528	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1137645	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11892236	0.80[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs11892443	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11902987	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12713264	0.88[CHB][hapmap]
rs12713265	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12713268	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12713269	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12713273	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs13386146	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs13391522	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs13391803	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13399656	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs13403284	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs13428703	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs17045939	0.88[CHB][hapmap]
rs17046061	0.80[AMR][1000 genomes]
rs17046067	0.80[AMR][1000 genomes]
rs17046077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17046097	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17046108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17046149	0.83[AMR][1000 genomes]
rs17046257	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs2048370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2229503	0.85[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2271329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3287	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs33946849	0.83[AMR][1000 genomes]
rs34311770	0.83[AMR][1000 genomes]
rs35619551	0.80[AMR][1000 genomes]
rs3739109	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796019	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs4346422	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs4455200	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs58419243	0.80[AMR][1000 genomes]
rs6545430	0.85[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs6545435	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs6545440	0.85[CEU][hapmap]
rs6706263	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6708082	0.85[CEU][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap]
rs6724136	0.81[EUR][1000 genomes]
rs6734445	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs6734536	0.85[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs6752720	0.85[CEU][hapmap]
rs6753004	0.85[CEU][hapmap]
rs72806653	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340302	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7556752	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7569127	0.88[CHB][hapmap]
rs7582640	0.85[CEU][hapmap]
rs7584223	0.85[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7599241	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs7608414	0.88[CHB][hapmap]

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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3850350	EML6	cis	Thyroid	GTEx
rs3850350	RPL23AP32	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54863000-54899400	Strong transcription	Primary T cells from cord blood	blood
2	chr2:54883000-54899400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:54891000-54899400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:54891200-54899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:54893200-54898800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:54893800-54899600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54893800-54900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:54894000-54899400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:54894000-54899600	Strong transcription	NH-A	brain
10	chr2:54894600-54898800	Strong transcription	Fetal Brain Female	brain
11	chr2:54894600-54902200	Weak transcription	Psoas Muscle	Psoas
12	chr2:54894800-54900400	Weak transcription	Small Intestine	intestine
13	chr2:54894800-54900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:54895200-54898800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:54895200-54900400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:54895400-54900200	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:54895400-54900400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr2:54895600-54899400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:54895800-54899800	Weak transcription	Right Atrium	heart
20	chr2:54895800-54900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:54895800-54900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:54895800-54902200	Weak transcription	Ovary	ovary
23	chr2:54896200-54899800	Weak transcription	Esophagus	oesophagus
24	chr2:54896600-54899200	Genic enhancers	HSMMtube	muscle
25	chr2:54896600-54899400	Genic enhancers	HSMM	muscle
26	chr2:54896800-54900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:54896800-54902400	Weak transcription	K562	blood
28	chr2:54897000-54900400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:54897000-54900600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54897000-54903800	Weak transcription	Brain Germinal Matrix	brain
31	chr2:54897200-54907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:54897400-54900600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:54897600-54898800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:54897600-54898800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:54897600-54899000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54897600-54899200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:54897600-54899400	Strong transcription	Fetal Lung	lung
38	chr2:54897600-54899800	Weak transcription	Stomach Mucosa	stomach
39	chr2:54897600-54900000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:54897600-54900200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:54897600-54900400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:54897600-54902800	Weak transcription	Gastric	stomach
43	chr2:54897800-54898800	Strong transcription	NHLF	lung
44	chr2:54897800-54899000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr2:54897800-54899000	Strong transcription	NHDF-Ad	bronchial
46	chr2:54897800-54899200	Weak transcription	Pancreas	Pancrea
47	chr2:54897800-54899600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:54897800-54899800	Weak transcription	Colonic Mucosa	Colon
49	chr2:54897800-54900200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:54897800-54901200	Strong transcription	A549	lung

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