Variant report

Variant	rs11712164
Chromosome Location	chr3:52244051-52244052
allele	A/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	MAX	chr3:52243987-52245042	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52244020-52245869	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52237147..52240103-chr3:52242583..52244871,3	MCF-7	breast:
2	chr3:52238883..52243786-chr3:52243916..52248823,6	K562	blood:
3	chr3:52230792..52233743-chr3:52243721..52245570,2	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs104903	0.83[ASN][1000 genomes]
rs164640	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs181274	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs187084	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs34569561	0.81[CHB][hapmap]
rs352139	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs352140	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs352158	0.86[CHB][hapmap]
rs352162	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs352163	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs352165	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs352166	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs352167	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs352168	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs352169	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs352170	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs352171	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs353551	0.85[CHB][hapmap]
rs3844291	0.83[JPT][hapmap]
rs3852064	0.82[JPT][hapmap]
rs411457	0.90[CHB][hapmap]
rs524986	0.86[CHB][hapmap]
rs614288	0.95[CHB][hapmap]
rs6802320	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7618915	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11712164	GLT8D1	cis	brain	seeQTL
rs11712164	GLT8D1	trans	brain	seeQTL
rs11712164	AD-017	cis	multi-tissue	Pritchard
rs11712164	FLJ12442	cis	multi-tissue	Pritchard
rs11712164	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52233000-52245200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:52233600-52249000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:52233600-52249200	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:52233600-52249600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:52233600-52250000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:52233600-52250000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:52233600-52250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:52233600-52250200	Strong transcription	Fetal Stomach	stomach
13	chr3:52233800-52249600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:52233800-52250000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr3:52233800-52250400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:52234400-52249800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr3:52234600-52249800	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:52234600-52249800	Strong transcription	HSMM	muscle
19	chr3:52234600-52249800	Strong transcription	HUVEC	blood vessel
20	chr3:52234600-52250000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr3:52234800-52251000	Strong transcription	Fetal Brain Female	brain
22	chr3:52235000-52250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:52235200-52246400	Strong transcription	NHDF-Ad	bronchial
24	chr3:52235200-52249200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:52235200-52249200	Strong transcription	Fetal Kidney	kidney
26	chr3:52235200-52249600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52235200-52249800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:52235400-52244200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:52235400-52249800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr3:52235400-52250000	Strong transcription	Brain Germinal Matrix	brain
31	chr3:52235400-52250400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:52235600-52244200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:52235600-52248600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:52235600-52250000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:52235800-52244200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52235800-52244200	Strong transcription	Fetal Lung	lung
37	chr3:52235800-52249400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:52235800-52249600	Strong transcription	Brain Anterior Caudate	brain
39	chr3:52235800-52249800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:52235800-52249800	Strong transcription	Brain Substantia Nigra	brain
41	chr3:52235800-52249800	Strong transcription	Fetal Thymus	thymus
42	chr3:52235800-52249800	Strong transcription	Dnd41	blood
43	chr3:52235800-52250000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:52235800-52250400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:52236000-52249800	Strong transcription	Primary T cells from cord blood	blood
46	chr3:52236200-52250200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:52236200-52250200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr3:52236200-52250200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:52236400-52248400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:52236400-52249400	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links