Variant report

Variant	rs422240
Chromosome Location	chr2:86852705-86852706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86667874..86671580-chr2:86848738..86852940,5	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015117	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs10169746	0.81[ASN][1000 genomes]
rs10184584	0.81[ASN][1000 genomes]
rs10184879	0.81[ASN][1000 genomes]
rs10187880	0.85[JPT][hapmap]
rs1080551	0.81[ASN][1000 genomes]
rs11127045	0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs11127047	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11689330	0.81[ASN][1000 genomes]
rs12328637	0.96[ASN][1000 genomes]
rs12613282	0.85[JPT][hapmap]
rs12614447	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs12615285	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs12623509	0.83[GIH][hapmap]
rs12714186	0.80[GIH][hapmap]
rs12714190	0.94[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs12714198	0.84[CHD][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs12714199	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12987172	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs12991654	0.81[ASN][1000 genomes]
rs13015620	0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs13034615	0.94[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs1518807	0.85[JPT][hapmap]
rs1629293	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]
rs218059	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2241803	0.93[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs2292887	0.88[MKK][hapmap];0.82[TSI][hapmap]
rs308900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs308902	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs308903	0.92[CEU][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs308910	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[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]
rs308912	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308914	1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs308915	0.81[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs308916	0.84[ASW][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes]
rs3201448	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs34666164	0.81[ASN][1000 genomes]
rs3755002	0.93[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832042	0.81[ASN][1000 genomes]
rs4832045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832300	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832302	0.81[ASN][1000 genomes]
rs4832304	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]
rs62147239	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547700	0.89[CEU][hapmap];0.85[GIH][hapmap]
rs6738663	0.90[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs6750226	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap]
rs6752371	0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs689912	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7570640	0.81[ASN][1000 genomes]
rs7584882	0.94[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap]
rs7596717	0.94[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap]
rs7601115	0.96[ASN][1000 genomes]
rs9284788	0.94[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap]
rs958561	0.86[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
rs422240	RNF103	cis	cerebellum	SCAN
rs422240	POLR1A	cis	parietal	SCAN
rs422240	PTCD3	cis	cerebellum	SCAN
rs422240	VPS24	cis	parietal	SCAN
rs422240	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs422240	POLR1A	cis	cerebellum	SCAN
rs422240	VPS24	cis	lymphoblastoid	seeQTL
rs422240	IMMT	cis	cerebellum	SCAN
rs422240	C2orf68	cis	cerebellum	SCAN

Chromatin state (count:41 , 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	chr2:86851400-86852800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:86851400-86853000	Enhancers	Brain Angular Gyrus	brain
10	chr2:86851400-86853200	Enhancers	Stomach Mucosa	stomach
11	chr2:86851400-86855400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:86851600-86852800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:86851600-86852800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:86851600-86852800	Enhancers	Colonic Mucosa	Colon
15	chr2:86851600-86852800	Enhancers	A549	lung
16	chr2:86851600-86853000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:86851600-86853000	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:86851600-86853000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr2:86851600-86853000	Enhancers	Brain Substantia Nigra	brain
20	chr2:86851600-86853000	Enhancers	HepG2	liver
21	chr2:86851600-86853200	Enhancers	Brain Anterior Caudate	brain
22	chr2:86851600-86854400	Weak transcription	Fetal Intestine Small	intestine
23	chr2:86851600-86854600	Weak transcription	Liver	Liver
24	chr2:86851600-86854600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:86851600-86854600	Weak transcription	Fetal Intestine Large	intestine
26	chr2:86851600-86854600	Weak transcription	Pancreas	Pancrea
27	chr2:86851600-86854600	Weak transcription	GM12878-XiMat	blood
28	chr2:86851600-86854800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:86851600-86855400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:86851600-86855400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:86851600-86856800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:86851600-86858600	Weak transcription	HMEC	breast
35	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:86852400-86858600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:86852600-86852800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:86852600-86852800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:86852600-86853200	Enhancers	Brain Hippocampus Middle	brain
41	chr2:86852600-86858600	Weak transcription	Fetal Muscle Leg	muscle

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