Variant report

Variant	rs352169
Chromosome Location	chr3:52236762-52236763
allele	C/T
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	NFIC	chr3:52236336-52237274	GM12878	blood:	n/a	n/a
2	MEF2C	chr3:52236532-52237211	GM12878	blood:	n/a	chr3:52236830-52236839 chr3:52236825-52236846 chr3:52236828-52236839 chr3:52236825-52236846 chr3:52236829-52236840 chr3:52236986-52237001
3	EBF1	chr3:52236600-52236857	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:52236464-52237232	GM12878	blood:	n/a	n/a
5	MEF2A	chr3:52236483-52237220	GM12878	blood:	n/a	chr3:52236830-52236839 chr3:52236825-52236846 chr3:52236828-52236839 chr3:52236825-52236846 chr3:52236829-52236840 chr3:52236986-52237001
6	POLR2A	chr3:52236306-52237147	HL-60	blood:	n/a	n/a
7	SPI1	chr3:52236397-52237026	GM12878	blood:	n/a	chr3:52236860-52236867 chr3:52236879-52236886 chr3:52236858-52236871
8	TBL1XR1	chr3:52236595-52237129	GM12878	blood:	n/a	n/a
9	NFATC1	chr3:52236294-52237048	GM12878	blood:	n/a	n/a
10	MTA3	chr3:52236312-52237148	GM12878	blood:	n/a	n/a
11	RUNX3	chr3:52236316-52237083	GM12878	blood:	n/a	n/a
12	MEF2A	chr3:52236499-52237241	GM12878	blood:	n/a	chr3:52236830-52236839 chr3:52236825-52236846 chr3:52236828-52236839 chr3:52236825-52236846 chr3:52236829-52236840 chr3:52236986-52237001
13	RUNX3	chr3:52236581-52237170	GM12878	blood:	n/a	n/a
14	SPI1	chr3:52236316-52237109	HL-60	blood:	n/a	chr3:52236860-52236867 chr3:52236879-52236886 chr3:52236858-52236871
15	ATF2	chr3:52236528-52237122	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:52236374-52237108	HL-60	blood:	n/a	n/a
17	STAT1	chr3:52236593-52236948	GM12878	blood:	n/a	n/a
18	IKZF1	chr3:52236448-52237119	GM12878	blood:	n/a	n/a
19	NFIC	chr3:52236610-52237278	GM12878	blood:	n/a	n/a
20	EBF1	chr3:52236422-52236858	GM12878	blood:	n/a	n/a
21	BCLAF1	chr3:52236427-52237246	GM12878	blood:	n/a	n/a
22	PML	chr3:52236448-52237215	GM12878	blood:	n/a	n/a
23	CEBPB	chr3:52236753-52237067	Hela-S3	cervix:	n/a	n/a
24	MYC	chr3:52236479-52237052	NB4	blood:	n/a	n/a
25	BCLAF1	chr3:52236459-52237068	GM12878	blood:	n/a	n/a
26	FOXM1	chr3:52236452-52237197	GM12878	blood:	n/a	n/a
27	MTA3	chr3:52236372-52237056	GM12878	blood:	n/a	n/a
28	SPI1	chr3:52236677-52236977	GM12878	blood:	n/a	chr3:52236860-52236867 chr3:52236879-52236886 chr3:52236858-52236871
29	MAZ	chr3:52236495-52236934	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:11603060..11603560-chr3:52236093..52236923,2	NB4	blood:
2	chr3:52230732..52234949-chr3:52236127..52239754,6	K562	blood:
3	chr3:52230039..52234196-chr3:52236127..52242387,6	K562	blood:
4	chr3:52235265..52238007-chr3:52238967..52240891,2	K562	blood:
5	chr3:52230948..52234705-chr3:52236612..52240056,5	MCF-7	breast:
6	chr3:52231540..52234351-chr3:52235459..52240031,5	MCF-7	breast:

Variant related genes	Relation type
ALAS1	TF binding region
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs104903	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717383	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs164640	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs181274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs352139	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs352140	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs352158	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs352161	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352163	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352165	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352166	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs352170	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs352171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs411457	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524986	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs614288	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6802320	0.90[ASN][1000 genomes]
rs730050	0.82[JPT][hapmap]
rs7614727	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7622851	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
10	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs352169	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs352169	GLT8D1	cis	brain	seeQTL
rs352169	SPCS1	cis	parietal	SCAN
rs352169	GLT8D1	trans	brain	seeQTL
rs352169	NEK4	cis	parietal	SCAN
rs352169	ITIH4	cis	parietal	SCAN
rs352169	RBM6	cis	cerebellum	SCAN
rs352169	GNL3	cis	cerebellum	SCAN
rs352169	DNAH1	cis	cerebellum	SCAN
rs352169	GNL3	cis	parietal	SCAN
rs352169	NT5DC2	cis	lymphoblastoid	seeQTL
rs352169	SEMA3G	cis	parietal	SCAN
rs352169	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs352169	NEK4	cis	cerebellum	SCAN
rs352169	FLJ12442	cis	multi-tissue	Pritchard
rs352169	GLYCTK	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52233000-52241600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:52233000-52245200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:52233400-52237000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:52233400-52237800	Genic enhancers	Primary B cells from cord blood	blood
5	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:52233600-52237000	Weak transcription	Stomach Mucosa	stomach
10	chr3:52233600-52238000	Strong transcription	HMEC	breast
11	chr3:52233600-52238800	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52233600-52239400	Strong transcription	Osteobl	bone
13	chr3:52233600-52249000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:52233600-52249200	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:52233600-52249600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52233600-52250000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:52233600-52250000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:52233600-52250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:52233600-52250200	Strong transcription	Fetal Stomach	stomach
20	chr3:52233800-52237200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:52233800-52238200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:52233800-52238200	Strong transcription	NHEK	skin
23	chr3:52233800-52249600	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:52233800-52250000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:52233800-52250400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52234200-52239600	Strong transcription	NH-A	brain
27	chr3:52234400-52236800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:52234400-52237000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:52234400-52237600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:52234400-52249800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:52234600-52237200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:52234600-52239800	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr3:52234600-52243200	Strong transcription	A549	lung
34	chr3:52234600-52249800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:52234600-52249800	Strong transcription	HSMM	muscle
36	chr3:52234600-52249800	Strong transcription	HUVEC	blood vessel
37	chr3:52234600-52250000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr3:52234800-52236800	Genic enhancers	HepG2	liver
39	chr3:52234800-52237200	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr3:52234800-52237200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr3:52234800-52238000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:52234800-52251000	Strong transcription	Fetal Brain Female	brain
43	chr3:52235000-52237000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:52235000-52237200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:52235000-52239000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:52235000-52250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:52235200-52237400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:52235200-52238200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:52235200-52240600	Transcr. at gene 5' and 3'	Liver	Liver
50	chr3:52235200-52242800	Strong transcription	K562	blood

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