Variant report

Variant	rs2545166
Chromosome Location	chr5:112213805-112213806
allele	C/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	chr5:112197996..112200677-chr5:112212037..112214219,2	K562	blood:

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1069061	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1093611	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs1093677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12656359	0.81[ASN][1000 genomes]
rs1441375	0.85[CEU][hapmap]
rs149192	0.90[JPT][hapmap]
rs151976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151978	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153546	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs153548	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs153550	0.84[EUR][1000 genomes]
rs153558	0.81[AMR][1000 genomes]
rs153562	0.82[AMR][1000 genomes]
rs1661035	0.88[CEU][hapmap]
rs173466	0.81[AMR][1000 genomes]
rs193527	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966477	0.83[ASN][1000 genomes]
rs2229992	0.84[CEU][hapmap]
rs2439591	0.83[CEU][hapmap]
rs2464805	0.83[CEU][hapmap]
rs2545162	0.88[CEU][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2545163	0.88[CEU][hapmap]
rs2545164	0.80[ASN][1000 genomes]
rs2545165	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2545167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545169	0.88[CEU][hapmap]
rs2546110	0.84[CEU][hapmap]
rs2909786	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2909787	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2909904	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909958	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2952615	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs351767	0.92[EUR][1000 genomes]
rs351769	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351770	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs351771	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs35726351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368575	0.82[JPT][hapmap]
rs372492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380144	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs382260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386830	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs392907	0.88[CEU][hapmap]
rs397768	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs41115	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs411356	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs419632	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42427	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs429427	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs430665	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs433429	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs434090	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434157	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs438252	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs439456	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442507	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs446567	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs448162	0.92[CEU][hapmap]
rs455412	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455469	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456313	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs458451	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459102	0.89[EUR][1000 genomes]
rs460301	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs460832	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461424	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs461866	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs463229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs464002	0.88[CEU][hapmap]
rs464708	0.87[CEU][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs465454	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465899	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs466443	0.93[CHB][hapmap];0.88[ASN][1000 genomes]
rs468101	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468610	0.83[EUR][1000 genomes]
rs468783	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468854	0.83[EUR][1000 genomes]
rs469663	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469727	0.84[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469827	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs481789	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs495794	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs497844	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs514763	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs519397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs563556	0.85[CEU][hapmap]
rs565453	0.93[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs565603	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs569940	0.81[ASN][1000 genomes]
rs580237	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs698405	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712662	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712663	0.86[EUR][1000 genomes]
rs712664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712665	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712666	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712671	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs818423	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818424	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs818425	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs818426	0.89[ASN][1000 genomes]
rs818427	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs818429	0.89[EUR][1000 genomes]
rs818782	0.84[ASN][1000 genomes]
rs864682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs866006	0.81[ASN][1000 genomes]
rs9011	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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
rs2545166	REEP5	cis	uninvolved skin	skin_eQTL
rs2545166	SRP19	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
4	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
8	chr5:112203600-112214400	Weak transcription	Stomach Mucosa	stomach
9	chr5:112205000-112214600	Weak transcription	Fetal Kidney	kidney
10	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112206400-112242800	Weak transcription	Fetal Brain Male	brain
12	chr5:112206600-112214000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:112206600-112214200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:112206600-112214400	Weak transcription	Hela-S3	cervix
15	chr5:112206600-112215400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:112206600-112215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:112206600-112216400	Weak transcription	Aorta	Aorta
18	chr5:112206600-112217200	Weak transcription	Right Ventricle	heart
19	chr5:112206600-112219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:112206600-112219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:112206800-112214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:112206800-112215400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:112206800-112215800	Weak transcription	Pancreas	Pancrea
24	chr5:112206800-112215800	Weak transcription	Spleen	Spleen
25	chr5:112206800-112217000	Weak transcription	Brain Angular Gyrus	brain
26	chr5:112206800-112217200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:112206800-112217200	Weak transcription	Gastric	stomach
28	chr5:112206800-112220800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:112206800-112220800	Weak transcription	Ovary	ovary
30	chr5:112207000-112215800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:112207000-112216000	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:112208200-112225800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:112209600-112214400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:112209600-112214400	Strong transcription	Fetal Thymus	thymus
35	chr5:112209600-112225000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:112209600-112226400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr5:112209600-112226800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:112209800-112214800	Strong transcription	Fetal Muscle Leg	muscle
39	chr5:112209800-112218600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:112209800-112224600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:112209800-112238600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:112210000-112214800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr5:112210000-112215000	Strong transcription	Primary B cells from cord blood	blood
44	chr5:112210200-112214400	Weak transcription	Thymus	Thymus
45	chr5:112210600-112218200	Weak transcription	Psoas Muscle	Psoas
46	chr5:112210600-112225000	Strong transcription	Liver	Liver
47	chr5:112210800-112225000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr5:112210800-112232400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr5:112211000-112214800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr5:112211200-112214200	Strong transcription	GM12878-XiMat	blood

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