Variant report

Variant	rs1406841
Chromosome Location	chr6:38576717-38576718
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484854	0.82[CHB][hapmap];0.86[MEX][hapmap]
rs10484856	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1073900	0.92[CEU][hapmap]
rs10947749	0.92[CEU][hapmap]
rs10947750	0.92[CEU][hapmap]
rs12154188	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12193868	0.92[CEU][hapmap];1.00[AFR][1000 genomes]
rs12198212	0.82[CHB][hapmap]
rs12198294	0.92[CEU][hapmap]
rs12199427	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes]
rs12206218	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12206371	0.92[CEU][hapmap]
rs12208087	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699015	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1699018	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17543429	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1781742	0.84[CEU][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs2748173	0.85[CHD][hapmap]
rs2814890	0.85[CHD][hapmap]
rs28616055	1.00[AFR][1000 genomes]
rs4074421	0.87[CEU][hapmap];1.00[AFR][1000 genomes]
rs4254983	0.92[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs55869483	1.00[AFR][1000 genomes]
rs6458060	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6903004	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927145	0.95[CEU][hapmap]
rs72853429	1.00[AFR][1000 genomes]
rs72856516	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7743871	0.87[CEU][hapmap]
rs7752239	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7755619	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7767041	0.92[CEU][hapmap]

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
rs1406841	ANKS1A	cis	cerebellum	SCAN
rs1406841	GLO1	cis	cerebellum	SCAN
rs1406841	GLO1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:38556000-38580400	Weak transcription	Ovary	ovary
3	chr6:38557400-38578000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:38560800-38580000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:38560800-38580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:38561400-38577600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:38561400-38578000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:38562000-38578000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:38562200-38580000	Weak transcription	Aorta	Aorta
10	chr6:38562800-38579800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:38564000-38580400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:38565400-38589200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:38565800-38583200	Weak transcription	Primary T cells from cord blood	blood
14	chr6:38565800-38583600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:38567800-38580400	Weak transcription	Right Ventricle	heart
16	chr6:38568200-38580000	Weak transcription	Psoas Muscle	Psoas
17	chr6:38568200-38584200	Weak transcription	Primary B cells from cord blood	blood
18	chr6:38571000-38580000	Weak transcription	Small Intestine	intestine
19	chr6:38571400-38577600	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:38571600-38581800	Weak transcription	Left Ventricle	heart
21	chr6:38572000-38577600	Weak transcription	Fetal Lung	lung
22	chr6:38572000-38578000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:38572000-38591600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:38572600-38577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:38572600-38579800	Weak transcription	NHLF	lung
26	chr6:38572800-38579800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:38572800-38581800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:38573000-38579800	Weak transcription	HSMMtube	muscle
29	chr6:38574800-38577800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:38576200-38579800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links