Variant report

Variant	rs308914
Chromosome Location	chr2:86857824-86857825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86855526..86858566-chr2:86929665..86933195,3	MCF-7	breast:
2	chr2:86849700..86853087-chr2:86854052..86858493,4	K562	blood:
3	chr2:86834891..86837645-chr2:86855817..86858466,2	MCF-7	breast:
4	chr2:86857823..86859880-chr2:86861018..86863511,2	MCF-7	breast:
5	chr2:86856951..86859444-chr2:86896714..86898569,2	MCF-7	breast:
6	chr2:86857369..86860425-chr2:86900280..86904256,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1015117	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs11127045	0.93[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs12614447	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs12615285	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs12623509	0.85[GIH][hapmap]
rs12714186	0.83[GIH][hapmap]
rs12714190	0.87[GIH][hapmap]
rs12714198	0.81[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs12987172	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs13015620	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs13034615	0.93[GIH][hapmap]
rs1629293	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]
rs218059	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2241803	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs2292887	0.81[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs308900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs308902	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs308903	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs308910	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308915	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs308916	0.84[ASW][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes]
rs3201448	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs3755002	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs422240	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]
rs4832045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4832300	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs4832304	0.87[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs62147239	0.85[EUR][1000 genomes]
rs6547700	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs6738663	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs6750226	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs6752371	0.87[GIH][hapmap]
rs689912	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7584882	0.87[GIH][hapmap]
rs7596717	0.87[GIH][hapmap]
rs9284788	0.95[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs958561	0.85[MKK][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs308914	POLR1A	cis	parietal	SCAN
rs308914	C2orf68	cis	cerebellum	SCAN
rs308914	POLR1A	cis	cerebellum	SCAN
rs308914	VPS24	cis	lymphoblastoid	seeQTL
rs308914	RNF103	cis	cerebellum	SCAN
rs308914	PTCD3	cis	cerebellum	SCAN
rs308914	VPS24	cis	parietal	SCAN
rs308914	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs308914	IMMT	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86851000-86860400	Weak transcription	Lung	lung
2	chr2:86851200-86858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:86851200-86860400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:86851600-86858600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:86851600-86858600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:86851600-86858600	Weak transcription	HMEC	breast
7	chr2:86851800-86860000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:86851800-86860400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:86852400-86858600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:86852600-86858600	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:86852800-86859000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:86853000-86859000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:86853000-86859400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:86853000-86859600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:86853000-86860400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:86853200-86860000	Weak transcription	Brain Anterior Caudate	brain
17	chr2:86854600-86858000	Enhancers	Fetal Intestine Large	intestine
18	chr2:86854800-86858400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:86855400-86858400	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:86855600-86858600	Weak transcription	Gastric	stomach
21	chr2:86855600-86858600	Weak transcription	Pancreas	Pancrea
22	chr2:86855600-86858800	Weak transcription	Small Intestine	intestine
23	chr2:86855800-86859000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:86856000-86860200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:86856200-86858000	Enhancers	Stomach Mucosa	stomach
26	chr2:86856200-86858600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:86856200-86858600	Weak transcription	A549	lung
28	chr2:86856600-86858600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:86856600-86860400	Weak transcription	Psoas Muscle	Psoas
30	chr2:86857200-86859000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:86857600-86858400	Weak transcription	Liver	Liver
32	chr2:86857600-86858600	Weak transcription	Colonic Mucosa	Colon
33	chr2:86857600-86858600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:86857800-86858600	Enhancers	HepG2	liver
35	chr2:86857800-86858800	Weak transcription	Fetal Intestine Small	intestine

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