Variant report

Variant	rs958561
Chromosome Location	chr2:86663548-86663549
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86661810..86665004-chr2:86667486..86670634,4	K562	blood:
2	chr2:86661917..86663938-chr2:86666698..86668736,2	MCF-7	breast:
3	chr2:86661810..86664020-chr2:86667060..86669461,3	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1015117	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs10169091	0.87[JPT][hapmap]
rs10178917	0.81[AMR][1000 genomes]
rs10180036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184879	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs10187880	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs1105865	0.82[CHB][hapmap]
rs11127034	0.95[ASN][1000 genomes]
rs11127045	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs1137684	0.81[EUR][1000 genomes]
rs12613282	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs12614447	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs12615285	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs12617075	0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes]
rs12623509	0.93[CEU][hapmap]
rs12714184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714186	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714198	0.93[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.85[YRI][hapmap]
rs12987172	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs13015620	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs13034615	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs13035266	0.85[AMR][1000 genomes]
rs13383096	0.87[AMR][1000 genomes]
rs1465813	0.84[EUR][1000 genomes]
rs1518807	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs1629293	0.88[MKK][hapmap]
rs2113607	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2241803	0.86[ASW][hapmap];0.93[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs2292887	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2367237	0.81[AMR][1000 genomes]
rs2367574	0.84[EUR][1000 genomes]
rs308914	0.85[MKK][hapmap]
rs3201448	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs3731812	0.81[EUR][1000 genomes]
rs3755002	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3770058	0.84[EUR][1000 genomes]
rs422240	0.86[MKK][hapmap]
rs4832282	0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes]
rs4832297	0.96[CEU][hapmap]
rs4832300	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs4832304	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs62150269	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6547685	0.82[CHB][hapmap]
rs6725080	0.83[EUR][1000 genomes]
rs6738663	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs6750226	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs6751871	0.82[CHB][hapmap]
rs6755760	0.82[CHB][hapmap]
rs766285	0.81[JPT][hapmap]
rs908791	0.85[AMR][1000 genomes]
rs9284788	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:2 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs958561	RNF103	cis	cerebellum	SCAN
rs958561	IMMT	cis	cerebellum	SCAN
rs958561	MAT2A	cis	parietal	SCAN
rs958561	PTCD3	cis	cerebellum	SCAN
rs958561	VPS24	cis	parietal	SCAN
rs958561	MRPL35	cis	parietal	SCAN
rs958561	POLR1A	cis	cerebellum	SCAN
rs958561	VPS24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86654000-86664400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:86663200-86663800	Enhancers	Ovary	ovary

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