Variant report

Variant	rs4832304
Chromosome Location	chr2:86830514-86830515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10169746	0.86[ASN][1000 genomes]
rs10180036	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs10184584	0.83[ASN][1000 genomes]
rs10184879	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10187753	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10187880	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1020306	0.81[EUR][1000 genomes]
rs10432704	0.84[ASN][1000 genomes]
rs1080551	0.86[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11127046	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11127047	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs1137684	0.82[EUR][1000 genomes]
rs11676576	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11684230	0.82[EUR][1000 genomes]
rs11689330	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689593	0.81[ASN][1000 genomes]
rs12328637	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12613282	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12615285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12623509	0.96[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12714186	0.96[CEU][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap]
rs12714188	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12714190	0.97[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12714199	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12987172	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12991654	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13015620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13390713	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13408041	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13429696	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1518807	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1629293	0.97[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2292887	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs308900	0.96[ASN][1000 genomes]
rs308902	0.82[GIH][hapmap]
rs308903	0.80[GIH][hapmap]
rs308910	0.85[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.87[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.91[GIH][hapmap]
rs3201448	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs34666164	0.86[ASN][1000 genomes]
rs3731812	0.82[EUR][1000 genomes]
rs3755002	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs422240	0.91[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs4832040	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832041	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832042	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4832043	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832045	0.83[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832299	0.88[EUR][1000 genomes]
rs4832300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832302	0.86[ASN][1000 genomes]
rs4832303	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62147239	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6728211	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6733569	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6750226	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6752371	0.97[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs689912	0.84[ASN][1000 genomes]
rs7369138	0.82[EUR][1000 genomes]
rs7570640	0.86[ASN][1000 genomes]
rs7584882	0.97[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7587034	0.82[ASN][1000 genomes]
rs7596717	0.97[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs7601115	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9284788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs958561	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4832304	RNF103	cis	cerebellum	SCAN
rs4832304	POLR1A	cis	parietal	SCAN
rs4832304	POLR1A	cis	cerebellum	SCAN
rs4832304	C2orf68	cis	cerebellum	SCAN
rs4832304	VPS24	cis	lymphoblastoid	seeQTL
rs4832304	PTCD3	cis	cerebellum	SCAN
rs4832304	VPS24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
2	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
5	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:86820600-86831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:86823000-86830600	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
9	chr2:86823600-86831200	Weak transcription	HSMMtube	muscle
10	chr2:86824000-86830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:86824000-86831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:86824600-86840600	Weak transcription	Fetal Heart	heart
13	chr2:86824800-86831000	Weak transcription	Left Ventricle	heart
14	chr2:86825400-86849000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:86825600-86830600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:86825800-86831000	Weak transcription	Liver	Liver
17	chr2:86826000-86831000	Weak transcription	HUVEC	blood vessel
18	chr2:86826400-86831000	Weak transcription	Hela-S3	cervix
19	chr2:86826600-86830800	Weak transcription	Primary T cells from cord blood	blood
20	chr2:86826600-86830800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:86826600-86830800	Weak transcription	Fetal Lung	lung
22	chr2:86826600-86830800	Weak transcription	HMEC	breast
23	chr2:86826600-86831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:86826600-86831000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:86826600-86831000	Weak transcription	Aorta	Aorta
26	chr2:86826600-86831000	Weak transcription	Gastric	stomach
27	chr2:86826800-86831000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:86826800-86831000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:86826800-86831200	Weak transcription	Right Ventricle	heart
30	chr2:86826800-86842000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:86826800-86847800	Weak transcription	NHEK	skin
32	chr2:86827000-86831000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:86827200-86831000	Weak transcription	Lung	lung
34	chr2:86827200-86831000	Weak transcription	K562	blood
35	chr2:86827200-86835600	Weak transcription	Brain Germinal Matrix	brain
36	chr2:86827400-86830600	Weak transcription	Adipose Nuclei	Adipose
37	chr2:86827600-86831000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:86827600-86831000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:86827600-86831000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:86827800-86830800	Weak transcription	Placenta	Placenta
41	chr2:86827800-86831000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:86827800-86831000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:86828200-86831000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:86828200-86831200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:86828200-86831200	Weak transcription	NHDF-Ad	bronchial
46	chr2:86828200-86847800	Weak transcription	NHLF	lung
47	chr2:86828400-86831000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:86828400-86831000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:86828400-86831000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:86828400-86831800	Strong transcription	Fetal Stomach	stomach

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