Variant report

Variant	rs3754270
Chromosome Location	chr1:85514841-85514842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12119445	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs12129308	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs1809248	0.84[EUR][1000 genomes]
rs4123223	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs473957	0.95[CEU][hapmap]
rs498429	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs504504	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs507465	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs536609	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs541897	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs597630	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs597704	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs600924	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs645435	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs654666	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs657309	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs673998	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs674647	0.96[CEU][hapmap];0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	esv3448123	chr1:85513114-85515312	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3754270	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL
rs3754270	LMO4	cis	cerebellum	SCAN
rs3754270	WDR63	cis	parietal	SCAN
rs3754270	MCOLN2	cis	Thyroid	GTEx
rs3754270	MCOLN2	cis	lymphoblastoid	seeQTL
rs3754270	MCOLN2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85512400-85515800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:85513000-85515000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:85513000-85515000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:85513000-85515800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:85513000-85515800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:85513200-85515000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:85513200-85515600	Active TSS	Pancreas	Pancrea
8	chr1:85513200-85515800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr1:85513400-85515000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:85513400-85515200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:85514200-85515600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr1:85514600-85515000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
13	chr1:85514600-85515200	Active TSS	Fetal Intestine Small	intestine
14	chr1:85514600-85515600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr1:85514600-85515800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:85514600-85516200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:85514600-85516600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr1:85514600-85516800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr1:85514600-85517600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:85514800-85515200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
21	chr1:85514800-85515200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr1:85514800-85515200	Bivalent Enhancer	Primary T cells from cord blood	blood
23	chr1:85514800-85515200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:85514800-85515200	Active TSS	Duodenum Mucosa	Duodenum
25	chr1:85514800-85515200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
26	chr1:85514800-85515200	Bivalent Enhancer	Fetal Kidney	kidney
27	chr1:85514800-85515800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr1:85514800-85515800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:85514800-85516400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr1:85514800-85527400	Weak transcription	Aorta	Aorta

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