Variant report

Variant	rs149130
Chromosome Location	chr5:112267095-112267096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112257473..112261765-chr5:112262739..112268514,7	K562	blood:
2	chr5:112262263..112263764-chr5:112265083..112267354,2	K562	blood:

Variant related genes	Relation type
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11241185	0.91[ASW][hapmap]
rs149190	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs149191	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149192	0.89[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs151979	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs151980	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs153544	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs153553	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153556	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153557	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153559	0.85[EUR][1000 genomes]
rs153560	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs153561	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153563	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153569	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154344	0.81[AMR][1000 genomes]
rs1625623	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1644099	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17135222	0.85[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289484	0.91[ASW][hapmap]
rs2431241	0.82[ASW][hapmap]
rs2431512	0.91[ASW][hapmap]
rs2464803	0.83[ASW][hapmap]
rs2545156	0.85[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2546106	0.91[ASW][hapmap]
rs2546108	0.82[ASW][hapmap]
rs2546110	0.91[ASW][hapmap]
rs3317	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs351768	0.85[CEU][hapmap]
rs368575	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs374613	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs382427	0.85[CEU][hapmap]
rs395858	0.88[CEU][hapmap]
rs396321	0.91[ASW][hapmap]
rs419155	0.83[ASW][hapmap];0.85[CEU][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs448162	0.83[ASW][hapmap]
rs454886	1.00[YRI][hapmap]
rs460137	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs467033	0.91[ASW][hapmap]
rs467660	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs469523	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs469675	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs469753	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469886	0.85[CEU][hapmap]
rs4705486	0.91[ASW][hapmap]
rs4705610	0.91[ASW][hapmap]
rs6594646	0.91[ASW][hapmap]
rs818428	0.85[CEU][hapmap]
rs818797	0.85[CEU][hapmap]
rs818799	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv2763866	chr5:112254282-112284223	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs149130	REEP5	cis	Esophagus Muscularis	GTEx
rs149130	NCRNA00219	cis	parietal	SCAN
rs149130	REEP5	cis	cerebellum	SCAN
rs149130	REEP5	Cis_1M	lymphoblastoid	RTeQTL
rs149130	MCC	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112258400-112287400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:112259000-112267200	Weak transcription	Psoas Muscle	Psoas
3	chr5:112259000-112267200	Weak transcription	Right Atrium	heart
4	chr5:112259000-112269200	Weak transcription	Osteobl	bone
5	chr5:112259600-112267600	Enhancers	Primary B cells from peripheral blood	blood
6	chr5:112262400-112267400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:112262400-112267600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr5:112262400-112267800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr5:112262600-112267600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:112263000-112267400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:112263200-112267600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:112263200-112268200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:112263400-112267400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:112263600-112267400	Enhancers	Fetal Thymus	thymus
15	chr5:112264000-112267400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:112264200-112267400	Enhancers	Thymus	Thymus
17	chr5:112265400-112267200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:112265400-112267400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr5:112265600-112267800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:112265800-112267400	Enhancers	Primary B cells from cord blood	blood
21	chr5:112265800-112267600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:112265800-112267800	Enhancers	Primary T cells from cord blood	blood
23	chr5:112265800-112267800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:112266000-112267400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:112266000-112267600	Enhancers	GM12878-XiMat	blood
26	chr5:112266000-112270800	Weak transcription	Placenta	Placenta
27	chr5:112266600-112267600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:112266600-112267600	Enhancers	Fetal Heart	heart
29	chr5:112266600-112267600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr5:112266800-112267800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr5:112267000-112267400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:112267000-112267400	Enhancers	Spleen	Spleen
33	chr5:112267000-112267400	Enhancers	NHLF	lung
34	chr5:112267000-112267600	Enhancers	K562	blood
35	chr5:112267000-112267600	Enhancers	NHDF-Ad	bronchial
36	chr5:112267000-112269400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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