Variant report

Variant	rs1629293
Chromosome Location	chr2:86853798-86853799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1015117	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs10169746	0.95[ASN][1000 genomes]
rs10184879	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10187880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10188515	0.85[ASN][1000 genomes]
rs1020306	0.80[ASN][1000 genomes]
rs10432704	0.93[ASN][1000 genomes]
rs1080551	0.95[ASN][1000 genomes]
rs11127045	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs11127046	0.88[ASN][1000 genomes]
rs1137684	0.80[ASN][1000 genomes]
rs11676576	0.88[ASN][1000 genomes]
rs11684230	0.80[ASN][1000 genomes]
rs11689330	0.95[ASN][1000 genomes]
rs11689593	0.91[ASN][1000 genomes]
rs12613282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12614447	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs12615285	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs12623509	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs12714186	0.83[GIH][hapmap]
rs12714188	0.88[ASN][1000 genomes]
rs12714190	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12714198	0.84[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap]
rs12714199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12987172	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs12991654	0.95[ASN][1000 genomes]
rs13015620	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs13034615	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs13390713	0.88[ASN][1000 genomes]
rs13408041	0.87[ASN][1000 genomes]
rs13429696	0.88[ASN][1000 genomes]
rs1518807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs218059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241803	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs2292887	0.81[GIH][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs308900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs308902	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs308903	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs308910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308912	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308914	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308915	0.81[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs308916	1.00[ASW][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes]
rs3201448	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs34666164	0.95[ASN][1000 genomes]
rs3731812	0.80[ASN][1000 genomes]
rs3755002	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs422240	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832040	0.87[ASN][1000 genomes]
rs4832042	0.94[ASN][1000 genomes]
rs4832045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4832296	0.88[ASN][1000 genomes]
rs4832297	0.88[ASN][1000 genomes]
rs4832299	0.81[ASN][1000 genomes]
rs4832300	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs4832302	0.95[ASN][1000 genomes]
rs4832304	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]
rs62147239	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6547700	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs6728211	0.93[ASN][1000 genomes]
rs6731025	0.82[ASN][1000 genomes]
rs6738663	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs6750226	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs6752371	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs689912	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7369138	0.80[ASN][1000 genomes]
rs7557796	0.88[CHB][hapmap]
rs7568840	0.88[CHB][hapmap]
rs7570640	0.95[ASN][1000 genomes]
rs7584882	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7593151	0.88[ASN][1000 genomes]
rs7596717	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8179729	0.88[ASN][1000 genomes]
rs9284788	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs958561	0.88[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv436305	chr2:86849862-86854021	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1629293	VPS24	cis	lymphoblastoid	seeQTL
rs1629293	PTCD3	cis	cerebellum	SCAN
rs1629293	POLR1A	cis	parietal	SCAN
rs1629293	C2orf68	cis	cerebellum	SCAN
rs1629293	POLR1A	cis	cerebellum	SCAN
rs1629293	VPS24	cis	parietal	SCAN
rs1629293	IMMT	cis	cerebellum	SCAN
rs1629293	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs1629293	RNF103	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86854800	Weak transcription	Gastric	stomach
2	chr2:86851000-86854800	Weak transcription	Small Intestine	intestine
3	chr2:86851000-86856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:86851000-86860400	Weak transcription	Lung	lung
5	chr2:86851200-86854800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:86851200-86858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:86851400-86855400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:86851600-86854400	Weak transcription	Fetal Intestine Small	intestine
10	chr2:86851600-86854600	Weak transcription	Liver	Liver
11	chr2:86851600-86854600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:86851600-86854600	Weak transcription	Fetal Intestine Large	intestine
13	chr2:86851600-86854600	Weak transcription	Pancreas	Pancrea
14	chr2:86851600-86854600	Weak transcription	GM12878-XiMat	blood
15	chr2:86851600-86854800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:86851600-86855400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:86851600-86855400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:86851600-86856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:86851600-86858600	Weak transcription	HMEC	breast
22	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:86852400-86858600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:86852600-86858600	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:86852800-86854600	Weak transcription	A549	lung
27	chr2:86852800-86855200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:86852800-86857200	Weak transcription	Colonic Mucosa	Colon
29	chr2:86852800-86859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:86853000-86854200	Weak transcription	HepG2	liver
31	chr2:86853000-86854800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:86853000-86859000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:86853000-86859400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:86853000-86859600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:86853200-86855400	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:86853200-86855600	Weak transcription	Stomach Mucosa	stomach
38	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain

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