Variant report

Variant	rs1866924
Chromosome Location	chr5:112026148-112026149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112025912..112028598-chr5:112039922..112042129,2	K562	blood:
2	chr5:112023980..112026718-chr5:112033004..112035530,2	K562	blood:
3	chr5:112024489..112026491-chr5:112028253..112031270,3	K562	blood:
4	chr5:112018990..112022293-chr5:112024063..112027716,5	K562	blood:
5	chr5:112023982..112026491-chr5:112028253..112030508,2	K562	blood:
6	chr5:112024407..112026277-chr5:112043233..112044928,2	K562	blood:
7	chr5:112025634..112029272-chr5:112039544..112043579,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10051624	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10071425	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10072068	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075281	0.92[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075323	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10075377	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10213844	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10463642	0.96[ASN][1000 genomes]
rs10477483	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241179	0.80[ASN][1000 genomes]
rs11241182	0.92[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11241183	0.84[EUR][1000 genomes]
rs11241185	0.92[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs11749632	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11749701	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12332692	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513787	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518091	0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs12655496	0.80[ASN][1000 genomes]
rs12658609	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659659	0.80[ASN][1000 genomes]
rs12719151	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs13156251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1441367	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530256	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17134858	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs17285505	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1914	0.85[CEU][hapmap]
rs1968557	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974786	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2019720	0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099810	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2229992	0.81[CHD][hapmap]
rs2289484	0.92[ASW][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs2431239	0.83[EUR][1000 genomes]
rs2431241	0.83[ASW][hapmap];0.85[CEU][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs2431512	0.92[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[LWK][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2439589	0.83[EUR][1000 genomes]
rs2464803	0.83[ASW][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap]
rs2545156	0.81[TSI][hapmap]
rs2546106	0.81[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs2546108	0.83[ASW][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs2546110	0.92[ASW][hapmap]
rs2546112	0.84[CHB][hapmap]
rs2546117	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs2707763	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2707765	0.82[EUR][1000 genomes]
rs28578275	0.84[EUR][1000 genomes]
rs2901844	0.83[EUR][1000 genomes]
rs3317	0.83[ASW][hapmap];0.81[TSI][hapmap]
rs35414976	0.83[EUR][1000 genomes]
rs374613	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs396321	0.92[ASW][hapmap]
rs414098	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs419155	0.83[ASW][hapmap];0.81[TSI][hapmap]
rs448162	0.83[ASW][hapmap];0.80[CHD][hapmap]
rs458906	0.81[EUR][1000 genomes]
rs460137	0.81[TSI][hapmap]
rs467033	0.92[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4705486	0.92[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4705559	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4705573	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705608	0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs4705610	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705624	0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs4705815	0.82[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs4705816	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs6594646	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6862050	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864688	0.83[EUR][1000 genomes]
rs6879057	0.82[EUR][1000 genomes]
rs6893949	0.82[EUR][1000 genomes]
rs7704618	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7719162	0.80[ASN][1000 genomes]
rs7727738	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733215	0.80[ASN][1000 genomes]
rs7733358	0.80[ASN][1000 genomes]
rs9326863	0.92[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs953916	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9647582	0.84[EUR][1000 genomes]
rs9647583	0.84[EUR][1000 genomes]
rs971517	0.83[EUR][1000 genomes]

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	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1866924	REEP5	cis	cerebellum	SCAN
rs1866924	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112021000-112026600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112021000-112026600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112021800-112030600	Weak transcription	Osteobl	bone
4	chr5:112022200-112026400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:112022600-112030600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:112024200-112027200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr5:112024200-112027800	Enhancers	K562	blood
8	chr5:112025400-112026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:112025600-112027000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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