Variant report

Variant	rs3766325
Chromosome Location	chr1:79128914-79128915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ELTD1-6	chr1:79127046-79129763	ENSG00000249107

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493611	0.87[ASN][1000 genomes]
rs11577395	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12409167	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547181	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56216300	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59610674	0.90[ASN][1000 genomes]
rs6424781	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669498	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6695058	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517942	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7523042	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526598	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7526782	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526927	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7530143	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533325	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7543088	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766325	ATP13A1	trans	parietal	SCAN
rs3766325	IFI44	Cis_1M	lymphoblastoid	RTeQTL
rs3766325	IFI44	cis	parietal	SCAN
rs3766325	FGD6	trans	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79116400-79129000	Weak transcription	Placenta	Placenta
2	chr1:79116400-79130000	Weak transcription	Stomach Mucosa	stomach
3	chr1:79117000-79132800	Weak transcription	Fetal Brain Male	brain
4	chr1:79117400-79129800	Weak transcription	NHLF	lung
5	chr1:79117400-79130400	Weak transcription	Pancreas	Pancrea
6	chr1:79117400-79130600	Weak transcription	Hela-S3	cervix
7	chr1:79117400-79131200	Weak transcription	HSMM	muscle
8	chr1:79117400-79144000	Weak transcription	Esophagus	oesophagus
9	chr1:79117400-79144000	Weak transcription	Spleen	Spleen
10	chr1:79117600-79129000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:79117600-79129400	Weak transcription	NH-A	brain
12	chr1:79117600-79153000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:79117800-79130200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:79118400-79130800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:79118400-79130800	Weak transcription	Small Intestine	intestine
16	chr1:79118600-79130800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:79119200-79129400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:79119200-79130800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:79119400-79129400	Weak transcription	Brain Germinal Matrix	brain
20	chr1:79119400-79129600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:79119400-79130400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:79119800-79130000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:79119800-79130800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:79119800-79130800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:79119800-79132600	Weak transcription	Right Ventricle	heart
26	chr1:79120000-79129400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:79120400-79130200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:79120600-79129200	Strong transcription	Fetal Lung	lung
29	chr1:79120600-79129400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:79120600-79130000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:79120600-79130200	Strong transcription	Liver	Liver
32	chr1:79120800-79130200	Strong transcription	Dnd41	blood
33	chr1:79121000-79129600	Weak transcription	Psoas Muscle	Psoas
34	chr1:79121600-79130000	Weak transcription	Fetal Stomach	stomach
35	chr1:79123200-79129200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:79124200-79129400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:79124400-79129000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:79124400-79129400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:79124400-79129400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:79124600-79129400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:79124600-79129400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:79124600-79129400	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:79124600-79129600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:79124600-79129600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:79124600-79129600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:79124800-79134000	Weak transcription	NHDF-Ad	bronchial
47	chr1:79125000-79130600	Strong transcription	Adipose Nuclei	Adipose
48	chr1:79125400-79133000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:79125600-79129600	Strong transcription	GM12878-XiMat	blood
50	chr1:79125800-79130000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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