Variant report

Variant	rs34762184
Chromosome Location	chr3:50541769-50541770
allele	A/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	MXI1	chr3:50539081-50541871	SK-N-SH	brain:	n/a	chr3:50539681-50539690

Variant related genes	Relation type
CACNA2D2	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1034405	0.89[CHD][hapmap]
rs1107265	0.82[CEU][hapmap]
rs11130255	1.00[YRI][hapmap]
rs12490042	0.88[CEU][hapmap]
rs12494849	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs13084476	0.88[ASN][1000 genomes]
rs13087550	0.88[CEU][hapmap]
rs13091933	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs13094336	1.00[YRI][hapmap]
rs13096264	1.00[YRI][hapmap]
rs13096772	1.00[YRI][hapmap]
rs1467913	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1467914	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs17787569	1.00[ASW][hapmap];0.89[CHD][hapmap];1.00[YRI][hapmap]
rs201198	0.89[CHD][hapmap]
rs2125369	1.00[YRI][hapmap]
rs2168866	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2236953	0.88[CEU][hapmap]
rs2236954	0.87[CEU][hapmap]
rs2236955	0.82[CEU][hapmap]
rs2236956	0.88[CEU][hapmap]
rs2236957	0.82[CEU][hapmap]
rs2236958	0.87[CEU][hapmap]
rs2236959	0.82[CEU][hapmap]
rs2236961	0.88[CEU][hapmap]
rs2236963	0.88[CEU][hapmap]
rs2236964	0.82[CEU][hapmap]
rs2236965	0.82[CEU][hapmap]
rs2236967	0.88[CEU][hapmap]
rs2236968	0.88[CEU][hapmap]
rs2236971	0.85[CEU][hapmap]
rs2236973	0.82[CEU][hapmap]
rs2236975	0.88[CEU][hapmap]
rs2236979	0.82[CEU][hapmap]
rs2236984	0.82[CEU][hapmap]
rs2236987	0.82[CEU][hapmap]
rs2236988	0.88[CEU][hapmap]
rs2282752	0.87[CEU][hapmap]
rs2282753	0.82[CEU][hapmap]
rs2282754	0.82[CEU][hapmap]
rs2282756	0.88[CEU][hapmap]
rs2282758	0.88[CEU][hapmap]
rs2298955	0.82[CEU][hapmap]
rs34267788	0.92[ASN][1000 genomes]
rs34434811	0.92[ASN][1000 genomes]
rs34584636	1.00[ASW][hapmap];0.89[CHD][hapmap];1.00[YRI][hapmap]
rs34704833	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34860383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35053615	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35198275	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35335661	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35684775	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35829757	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35864641	0.92[ASN][1000 genomes]
rs35908181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35986136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36046126	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36059704	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3804628	1.00[YRI][hapmap]
rs399484	0.89[CHD][hapmap]
rs4533647	0.92[ASN][1000 genomes]
rs4688719	0.94[CEU][hapmap]
rs57361338	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58432784	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61018691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61423002	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6786523	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs6787521	1.00[YRI][hapmap]
rs6787890	0.88[CEU][hapmap]
rs6791880	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6792502	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6807916	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71326934	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73082948	0.92[ASN][1000 genomes]
rs734767	0.82[CEU][hapmap]
rs73835511	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73835517	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743756	0.82[CEU][hapmap]
rs743757	0.82[CEU][hapmap]
rs743857	0.82[CEU][hapmap]
rs7613931	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs762895	0.88[CEU][hapmap]
rs762897	0.94[CEU][hapmap]
rs762898	0.88[CEU][hapmap]
rs763030	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs916217	0.88[CEU][hapmap]
rs929047	0.88[CEU][hapmap]
rs9835537	0.82[CEU][hapmap]
rs9867588	1.00[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv3375288	chr3:50539473-50542821	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34762184	PARP3	cis	parietal	SCAN
rs34762184	CAMP	cis	cerebellum	SCAN
rs34762184	APEH	cis	cerebellum	SCAN
rs34762184	HYAL2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50540200-50541800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:50540600-50541800	Weak transcription	Fetal Lung	lung
3	chr3:50540800-50541800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr3:50541200-50541800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:50541200-50541800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:50541200-50541800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:50541200-50541800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr3:50541200-50541800	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr3:50541200-50541800	Enhancers	Gastric	stomach
10	chr3:50541400-50541800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr3:50541400-50541800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:50541400-50541800	Bivalent Enhancer	Fetal Thymus	thymus
13	chr3:50541400-50541800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr3:50541400-50541800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr3:50541400-50542200	Bivalent Enhancer	Placenta	Placenta
16	chr3:50541600-50541800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr3:50541600-50541800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:50541600-50541800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:50541600-50541800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
20	chr3:50541600-50541800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr3:50541600-50541800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr3:50541600-50541800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:50541600-50541800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr3:50541600-50541800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr3:50541600-50541800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:50541600-50541800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:50541600-50541800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
28	chr3:50541600-50541800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:50541600-50541800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:50541600-50541800	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr3:50541600-50541800	Bivalent Enhancer	Brain Hippocampus Middle	brain
32	chr3:50541600-50541800	Enhancers	Colon Smooth Muscle	Colon
33	chr3:50541600-50541800	Enhancers	Fetal Stomach	stomach
34	chr3:50541600-50541800	Enhancers	Lung	lung
35	chr3:50541600-50542000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr3:50541600-50542000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr3:50541600-50542000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:50541600-50542000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:50541600-50542000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:50541600-50542200	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:50541600-50552200	Weak transcription	Spleen	Spleen

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