Variant report

Variant	rs3850429
Chromosome Location	chr1:85464736-85464737
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85459671-85465061	GM12892	blood:	n/a	n/a
2	TCF7L2	chr1:85463483-85464827	PANC-1	pancreas:	n/a	n/a
3	EBF1	chr1:85464485-85464813	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:85461494-85464994	GM12892	blood:	n/a	n/a
5	CTCF	chr1:85464700-85464850	GM12875	blood:	n/a	n/a
6	CTCF	chr1:85464720-85464870	GM12865	blood:	n/a	n/a
7	CEBPB	chr1:85464657-85464820	IMR90	lung:	n/a	n/a
8	ZNF143	chr1:85464457-85464793	GM12878	blood:	n/a	n/a
9	MTA3	chr1:85464165-85465112	GM12878	blood:	n/a	n/a
10	WRNIP1	chr1:85464037-85465106	GM12878	blood:	n/a	n/a
11	RUNX3	chr1:85464567-85464877	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:85464539-85464999	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:85459795-85464999	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:85460981-85465011	GM19099	blood:	n/a	n/a
15	CTCF	chr1:85464720-85464870	GM06990	blood:	n/a	n/a
16	POLR2A	chr1:85464372-85464883	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:85461099-85464971	GM19193	blood:	n/a	n/a
18	CEBPB	chr1:85464587-85464939	H1-hESC	embryonic stem cell:	n/a	n/a
19	SUZ12	chr1:85461677-85465137	NT2-D1	testis:	n/a	n/a
20	CTCF	chr1:85464718-85464966	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:85461512-85464970	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:85464493-85464944	GM12892	blood:	n/a	n/a
23	NRF1	chr1:85464515-85464873	GM12878	blood:	n/a	n/a
24	SPI1	chr1:85464634-85464853	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
MCOLN2	TF binding region
WDR63	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11161500	0.96[ASN][1000 genomes]
rs11799554	0.88[ASN][1000 genomes]
rs11800103	0.86[ASN][1000 genomes]
rs12119445	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12129308	0.84[ASN][1000 genomes]
rs12140467	0.86[ASN][1000 genomes]
rs12146119	0.86[ASN][1000 genomes]
rs2031480	0.86[ASN][1000 genomes]
rs4123223	0.98[ASN][1000 genomes]
rs472373	0.81[ASN][1000 genomes]
rs473957	0.83[ASN][1000 genomes]
rs4907015	0.86[ASN][1000 genomes]
rs4907117	0.80[AMR][1000 genomes]
rs498429	0.81[ASN][1000 genomes]
rs504504	0.81[ASN][1000 genomes]
rs521435	0.83[ASN][1000 genomes]
rs522195	0.83[ASN][1000 genomes]
rs536609	0.85[ASN][1000 genomes]
rs541897	0.85[ASN][1000 genomes]
rs550766	0.81[ASN][1000 genomes]
rs55997821	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs574954	0.85[ASN][1000 genomes]
rs591772	0.81[ASN][1000 genomes]
rs593721	0.85[ASN][1000 genomes]
rs593745	0.85[ASN][1000 genomes]
rs597630	0.81[ASN][1000 genomes]
rs597704	0.83[ASN][1000 genomes]
rs600924	0.85[ASN][1000 genomes]
rs613190	0.81[ASN][1000 genomes]
rs615161	0.81[ASN][1000 genomes]
rs632623	0.82[ASN][1000 genomes]
rs640149	0.85[ASN][1000 genomes]
rs645435	0.81[ASN][1000 genomes]
rs652272	0.83[ASN][1000 genomes]
rs654662	0.85[ASN][1000 genomes]
rs654666	0.85[ASN][1000 genomes]
rs657309	0.85[ASN][1000 genomes]
rs6576739	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs658658	0.85[ASN][1000 genomes]
rs666515	0.85[ASN][1000 genomes]
rs668263	0.85[ASN][1000 genomes]
rs671852	0.85[ASN][1000 genomes]
rs672202	0.85[ASN][1000 genomes]
rs673998	0.83[ASN][1000 genomes]
rs674182	0.83[ASN][1000 genomes]
rs674647	0.83[ASN][1000 genomes]
rs67529032	0.95[ASN][1000 genomes]
rs688208	0.82[ASN][1000 genomes]
rs7537383	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3850429	MCOLN2	cis	Thyroid	GTEx
rs3850429	MCOLN2	cis	multi-tissue	Pritchard
rs3850429	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85463000-85464800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
2	chr1:85463000-85464800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:85463200-85464800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
4	chr1:85463200-85464800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:85463400-85465000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr1:85463800-85464800	Bivalent/Poised TSS	NHEK	skin
7	chr1:85464000-85464800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
8	chr1:85464000-85465000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:85464200-85464800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:85464200-85464800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr1:85464200-85464800	Flanking Active TSS	GM12878-XiMat	blood
12	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:85464400-85464800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:85464400-85464800	Bivalent Enhancer	Brain Anterior Caudate	brain
15	chr1:85464400-85464800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
16	chr1:85464400-85465000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:85464400-85465000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:85464400-85465000	Bivalent Enhancer	NH-A	brain
19	chr1:85464400-85466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:85464600-85464800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr1:85464600-85464800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:85464600-85464800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:85464600-85464800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr1:85464600-85464800	Bivalent Enhancer	Primary T cells from cord blood	blood
25	chr1:85464600-85464800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:85464600-85464800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
27	chr1:85464600-85464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:85464600-85464800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
29	chr1:85464600-85464800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:85464600-85464800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:85464600-85464800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:85464600-85464800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
33	chr1:85464600-85465000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
34	chr1:85464600-85465000	Bivalent Enhancer	Fetal Brain Male	brain
35	chr1:85464600-85465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:85464600-85465200	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--

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