Variant report

Variant	rs4392718
Chromosome Location	chr6:38494062-38494063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38492262..38495256-chr6:38538776..38541740,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10807196	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10807198	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10947740	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10947752	0.82[EUR][1000 genomes]
rs1321056	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1699001	0.96[CEU][hapmap]
rs1699002	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs1699003	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs1699007	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs1739626	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs1739627	0.96[CEU][hapmap]
rs1739628	0.80[EUR][1000 genomes]
rs1739629	0.80[EUR][1000 genomes]
rs1739632	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1739633	0.82[ASW][hapmap]
rs1781708	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs1852979	0.82[EUR][1000 genomes]
rs2092797	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2144328	0.85[CEU][hapmap]
rs2180104	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252550	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs2474245	0.86[ASN][1000 genomes]
rs2748157	0.81[ASN][1000 genomes]
rs2748164	0.97[ASN][1000 genomes]
rs2748165	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2748172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814883	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814885	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2814889	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2814894	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4236060	0.82[ASW][hapmap]
rs55949948	0.97[ASN][1000 genomes]
rs6458059	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6923737	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6931131	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6932235	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7740763	0.83[JPT][hapmap]
rs910516	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs9394508	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4392718	GLO1	cis	parietal	SCAN
rs4392718	GLO1	cis	cerebellum	SCAN
rs4392718	BYSL	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38476600-38499800	Weak transcription	Pancreas	Pancrea
4	chr6:38476800-38498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:38477800-38498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:38478000-38494800	Weak transcription	Fetal Kidney	kidney
7	chr6:38479000-38509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:38485200-38496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:38485400-38500400	Weak transcription	Gastric	stomach
10	chr6:38485800-38495600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:38486400-38495600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:38487000-38518600	Weak transcription	Primary T cells from cord blood	blood
13	chr6:38487800-38502600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:38489000-38501000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:38490200-38499600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:38490400-38497800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:38490600-38495800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:38490600-38496200	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:38490600-38503400	Weak transcription	Fetal Lung	lung
20	chr6:38492800-38508000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:38493000-38495000	Weak transcription	Osteobl	bone
22	chr6:38493000-38495800	Weak transcription	NH-A	brain
23	chr6:38493400-38494800	Strong transcription	Ovary	ovary
24	chr6:38493400-38496400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:38493600-38494200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:38493600-38494200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr6:38493600-38494400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr6:38493600-38494400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
29	chr6:38493600-38494400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr6:38493600-38498600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr6:38493800-38494200	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr6:38493800-38494200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr6:38493800-38494400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:38493800-38494400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:38493800-38494400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:38493800-38494400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
37	chr6:38493800-38494400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
38	chr6:38493800-38494400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:38493800-38494400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:38493800-38494400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:38493800-38494400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:38493800-38494400	ZNF genes & repeats	Aorta	Aorta
43	chr6:38493800-38494400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr6:38493800-38494400	ZNF genes & repeats	Fetal Stomach	stomach
45	chr6:38493800-38494400	ZNF genes & repeats	Left Ventricle	heart
46	chr6:38493800-38494400	ZNF genes & repeats	Lung	lung
47	chr6:38493800-38494400	ZNF genes & repeats	Spleen	Spleen
48	chr6:38493800-38494800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr6:38493800-38495000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
50	chr6:38494000-38494200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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