Variant report

Variant	rs352170
Chromosome Location	chr3:52236077-52236078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52235265..52238007-chr3:52238967..52240891,2	K562	blood:
2	chr3:52231540..52234351-chr3:52235459..52240031,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs104903	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[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];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs181274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs352139	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs352140	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs352158	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352161	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352163	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352165	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352166	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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352168	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352169	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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs411457	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[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];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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];0.88[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6802320	0.89[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: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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs352170	AD-017	cis	multi-tissue	Pritchard
rs352170	GLYCTK	cis	multi-tissue	Pritchard
rs352170	FLJ12442	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52233000-52236200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:52233000-52236400	Weak transcription	Aorta	Aorta
3	chr3:52233000-52241600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52233000-52245200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52233400-52236400	Weak transcription	Ovary	ovary
6	chr3:52233400-52236600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:52233400-52237000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr3:52233400-52237800	Genic enhancers	Primary B cells from cord blood	blood
9	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:52233600-52236200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:52233600-52236200	Weak transcription	Gastric	stomach
15	chr3:52233600-52236200	Weak transcription	Lung	lung
16	chr3:52233600-52236200	Weak transcription	Spleen	Spleen
17	chr3:52233600-52236400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:52233600-52236400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:52233600-52236400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:52233600-52236400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:52233600-52236400	Weak transcription	Esophagus	oesophagus
22	chr3:52233600-52236400	Weak transcription	Fetal Brain Male	brain
23	chr3:52233600-52236400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:52233600-52236400	Weak transcription	Psoas Muscle	Psoas
25	chr3:52233600-52236400	Weak transcription	Right Ventricle	heart
26	chr3:52233600-52236600	Weak transcription	Pancreas	Pancrea
27	chr3:52233600-52236600	Weak transcription	Thymus	Thymus
28	chr3:52233600-52237000	Weak transcription	Stomach Mucosa	stomach
29	chr3:52233600-52238000	Strong transcription	HMEC	breast
30	chr3:52233600-52238800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:52233600-52239400	Strong transcription	Osteobl	bone
32	chr3:52233600-52249000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:52233600-52249200	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:52233600-52249600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:52233600-52250000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:52233600-52250000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52233600-52250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:52233600-52250200	Strong transcription	Fetal Stomach	stomach
39	chr3:52233800-52236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:52233800-52236400	Weak transcription	Brain Angular Gyrus	brain
41	chr3:52233800-52236400	Weak transcription	Colonic Mucosa	Colon
42	chr3:52233800-52236400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:52233800-52236400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:52233800-52236600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:52233800-52236600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:52233800-52236600	Weak transcription	Fetal Heart	heart
47	chr3:52233800-52236600	Weak transcription	Small Intestine	intestine
48	chr3:52233800-52237200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:52233800-52238200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:52233800-52238200	Strong transcription	NHEK	skin

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