Variant report

Variant	rs2304641
Chromosome Location	chr1:85513398-85513399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10443172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11808352	0.91[YRI][hapmap]
rs12024977	0.93[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12028736	0.98[ASN][1000 genomes]
rs12030730	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12030837	0.92[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs12037219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12041012	0.99[ASN][1000 genomes]
rs12042160	0.96[ASN][1000 genomes]
rs1371140	1.00[JPT][hapmap]
rs1371143	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1837329	0.83[EUR][1000 genomes]
rs2028304	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2083283	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2840050	0.93[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs61769366	0.81[ASN][1000 genomes]
rs61770879	0.96[ASN][1000 genomes]
rs6665436	0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs6672362	0.84[CHB][hapmap]
rs6679539	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6688354	0.96[ASN][1000 genomes]
rs6690464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs6690583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs6700723	0.99[ASN][1000 genomes]
rs7522239	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs7540706	0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs7545349	0.91[YRI][hapmap]
rs7547224	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7547317	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs893618	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs898036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2304641	MCOLN2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85512400-85515800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:85512600-85513400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr1:85512800-85513400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:85512800-85513600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr1:85512800-85513600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
6	chr1:85512800-85513600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr1:85512800-85513600	Bivalent Enhancer	Fetal Lung	lung
8	chr1:85512800-85513600	Active TSS	Right Atrium	heart
9	chr1:85512800-85513600	Flanking Active TSS	HMEC	breast
10	chr1:85512800-85514600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
11	chr1:85512800-85514800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
12	chr1:85513000-85513400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr1:85513000-85513400	Bivalent Enhancer	Brain Anterior Caudate	brain
14	chr1:85513000-85513400	Bivalent/Poised TSS	Colonic Mucosa	Colon
15	chr1:85513000-85513400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr1:85513000-85513400	Bivalent Enhancer	Fetal Heart	heart
17	chr1:85513000-85513400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr1:85513000-85513400	Bivalent Enhancer	Left Ventricle	heart
19	chr1:85513000-85513400	Bivalent Enhancer	Lung	lung
20	chr1:85513000-85513400	Enhancers	Ovary	ovary
21	chr1:85513000-85513400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
22	chr1:85513000-85513400	Bivalent/Poised TSS	NHDF-Ad	bronchial
23	chr1:85513000-85513600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:85513000-85513600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr1:85513000-85513600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
26	chr1:85513000-85513600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr1:85513000-85513600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:85513000-85513600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:85513000-85513600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:85513000-85513600	Bivalent Enhancer	Esophagus	oesophagus
31	chr1:85513000-85513600	Bivalent/Poised TSS	Fetal Kidney	kidney
32	chr1:85513000-85513600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
33	chr1:85513000-85513600	Bivalent Enhancer	Small Intestine	intestine
34	chr1:85513000-85513800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:85513000-85513800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:85513000-85513800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:85513000-85513800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
38	chr1:85513000-85514200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr1:85513000-85514200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:85513000-85514200	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr1:85513000-85514400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:85513000-85514400	Active TSS	Duodenum Mucosa	Duodenum
43	chr1:85513000-85514400	Active TSS	Right Ventricle	heart
44	chr1:85513000-85514600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:85513000-85514600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:85513000-85514800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
48	chr1:85513000-85514800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:85513000-85515000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr1:85513000-85515000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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