Variant report

Variant	rs514763
Chromosome Location	chr5:112215156-112215157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112213045..112215334-chr5:112215360..112217961,2	K562	blood:
2	chr5:112213405..112216248-chr5:112216805..112218995,2	K562	blood:
3	chr5:112214521..112217440-chr5:112219552..112222525,2	MCF-7	breast:
4	chr5:112214124..112215918-chr5:112256466..112258811,2	MCF-7	breast:
5	chr5:112204419..112206839-chr5:112213966..112216300,2	K562	blood:
6	chr5:112210185..112212366-chr5:112214528..112217503,2	K562	blood:
7	chr5:112195269..112200241-chr5:112214225..112218967,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249947	Chromatin interaction
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1069061	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs1093611	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1093677	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs1441375	0.81[CEU][hapmap]
rs149193	0.86[ASN][1000 genomes]
rs151976	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs151977	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs151978	0.88[EUR][1000 genomes]
rs153544	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs153545	0.84[EUR][1000 genomes]
rs153546	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153548	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs153549	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs153550	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153551	0.93[ASN][1000 genomes]
rs153552	0.91[ASN][1000 genomes]
rs154344	0.87[ASN][1000 genomes]
rs1661035	0.84[CEU][hapmap]
rs193527	0.83[EUR][1000 genomes]
rs2545155	0.82[ASN][1000 genomes]
rs2545156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2545162	0.84[CEU][hapmap]
rs2545163	0.88[CEU][hapmap]
rs2545166	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2545167	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs2545169	0.84[CEU][hapmap]
rs2545170	0.94[ASN][1000 genomes]
rs2546108	0.85[CHB][hapmap]
rs2546112	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs2546115	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs2707765	0.80[CHB][hapmap]
rs2909904	0.94[EUR][1000 genomes]
rs3317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351767	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs351769	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs351770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35726351	0.94[EUR][1000 genomes]
rs368575	0.94[ASN][1000 genomes]
rs372492	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs373059	0.82[ASN][1000 genomes]
rs374613	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs380144	0.88[EUR][1000 genomes]
rs382260	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs382427	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs392907	0.84[CEU][hapmap]
rs395858	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs410701	0.94[ASN][1000 genomes]
rs41116	0.84[ASN][1000 genomes]
rs411356	0.84[CEU][hapmap]
rs414098	0.81[CHB][hapmap]
rs419155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs419632	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs429427	0.80[CEU][hapmap]
rs430665	0.88[EUR][1000 genomes]
rs431287	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs434090	0.88[EUR][1000 genomes]
rs434157	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs438252	0.93[EUR][1000 genomes]
rs439456	0.87[EUR][1000 genomes]
rs446567	0.88[EUR][1000 genomes]
rs448162	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs448475	0.84[ASN][1000 genomes]
rs448613	0.94[ASN][1000 genomes]
rs454968	0.85[ASN][1000 genomes]
rs455412	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs455469	0.86[EUR][1000 genomes]
rs456313	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs456531	0.95[ASN][1000 genomes]
rs458451	0.88[EUR][1000 genomes]
rs459102	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs460137	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs460301	0.93[EUR][1000 genomes]
rs460832	0.88[EUR][1000 genomes]
rs461424	0.86[EUR][1000 genomes]
rs461866	0.80[EUR][1000 genomes]
rs463229	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs464002	0.84[CEU][hapmap]
rs464708	0.83[CEU][hapmap]
rs465454	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs468101	0.81[EUR][1000 genomes]
rs468610	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs468751	0.88[ASN][1000 genomes]
rs468783	0.87[EUR][1000 genomes]
rs468854	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469663	0.83[EUR][1000 genomes]
rs469727	0.83[EUR][1000 genomes]
rs469760	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs469827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs469886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4705624	0.80[CHB][hapmap]
rs495794	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505382	0.88[ASN][1000 genomes]
rs519397	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs563556	0.81[CEU][hapmap]
rs566419	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs580237	0.88[EUR][1000 genomes]
rs67293732	0.95[ASN][1000 genomes]
rs698405	0.84[EUR][1000 genomes]
rs712662	0.88[EUR][1000 genomes]
rs712663	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712664	0.91[EUR][1000 genomes]
rs712665	0.88[EUR][1000 genomes]
rs712666	0.85[EUR][1000 genomes]
rs712668	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs712670	0.94[ASN][1000 genomes]
rs712671	0.88[EUR][1000 genomes]
rs7213	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818423	0.91[EUR][1000 genomes]
rs818424	0.84[EUR][1000 genomes]
rs818425	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs818427	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs818428	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs818429	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818430	0.95[ASN][1000 genomes]
rs818797	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs864682	0.93[EUR][1000 genomes]
rs9011	0.92[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs514763	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs514763	REEP5	cis	uninvolved skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
6	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
8	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:112206600-112216400	Weak transcription	Aorta	Aorta
11	chr5:112206600-112217200	Weak transcription	Right Ventricle	heart
12	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:112206800-112215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:112206800-112215800	Weak transcription	Pancreas	Pancrea
16	chr5:112206800-112215800	Weak transcription	Spleen	Spleen
17	chr5:112206800-112217000	Weak transcription	Brain Angular Gyrus	brain
18	chr5:112206800-112217200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:112206800-112217200	Weak transcription	Gastric	stomach
20	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:112206800-112220800	Weak transcription	Ovary	ovary
22	chr5:112207000-112215800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:112207000-112216000	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:112209800-112218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:112210600-112218200	Weak transcription	Psoas Muscle	Psoas
32	chr5:112210600-112225000	Strong transcription	Liver	Liver
33	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr5:112211200-112216600	Strong transcription	NHDF-Ad	bronchial
36	chr5:112211200-112222600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:112211200-112240000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr5:112211400-112216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:112211600-112217200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:112211600-112256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:112211800-112215200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:112211800-112215200	Weak transcription	Fetal Intestine Small	intestine
43	chr5:112211800-112223400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:112211800-112239200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr5:112212200-112216400	Genic enhancers	Dnd41	blood
46	chr5:112212200-112256400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:112212400-112215200	Weak transcription	Lung	lung
48	chr5:112212400-112220200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:112212400-112225200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:112212400-112225400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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