Variant report

Variant	rs544243
Chromosome Location	chr5:112167130-112167131
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10073398	0.84[EUR][1000 genomes]
rs10076641	0.81[EUR][1000 genomes]
rs1069061	0.85[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11954856	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12513804	0.85[CEU][hapmap]
rs12656359	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12659119	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12719151	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs1465910	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1734243	0.89[ASN][1000 genomes]
rs1816769	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2020383	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2289484	0.81[EUR][1000 genomes]
rs2431238	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs2431240	0.86[AMR][1000 genomes]
rs2431242	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2439591	0.87[MEX][hapmap]
rs2464805	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap]
rs2545159	0.87[ASN][1000 genomes]
rs2545162	0.81[MEX][hapmap]
rs2545163	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2545169	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs2546111	0.96[ASN][1000 genomes]
rs2707763	0.81[EUR][1000 genomes]
rs2909786	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909787	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909958	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35130225	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351771	0.81[MEX][hapmap]
rs380144	0.85[ASN][1000 genomes]
rs3846716	0.82[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs392907	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs395266	0.92[ASN][1000 genomes]
rs396321	0.81[CEU][hapmap]
rs401908	0.88[ASN][1000 genomes]
rs4099181	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41115	0.81[MEX][hapmap]
rs411356	0.81[MEX][hapmap]
rs414098	0.81[CEU][hapmap]
rs42427	0.81[MEX][hapmap]
rs434157	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs438252	0.85[ASN][1000 genomes]
rs458967	0.93[ASN][1000 genomes]
rs459552	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs464708	0.81[MEX][hapmap]
rs465899	0.81[MEX][hapmap]
rs4705609	0.82[EUR][1000 genomes]
rs4705815	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs501250	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs529076	0.92[ASN][1000 genomes]
rs548710	0.81[EUR][1000 genomes]
rs563556	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs569940	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62364017	0.83[EUR][1000 genomes]
rs6864688	0.82[CEU][hapmap]
rs6867243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6894351	0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6898133	0.81[CEU][hapmap]
rs818427	0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs861674	0.89[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9326862	0.89[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs9326863	0.85[CEU][hapmap];0.81[TSI][hapmap]

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	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs544243	REEP5	cis	cerebellum	SCAN
rs544243	NCRNA00219	cis	parietal	SCAN
rs544243	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
12	chr5:112152000-112183800	Weak transcription	Gastric	stomach
13	chr5:112152200-112172000	Weak transcription	NHLF	lung
14	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
18	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
20	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
21	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
23	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
24	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
27	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:112158600-112173200	Weak transcription	Fetal Kidney	kidney
29	chr5:112158800-112173400	Weak transcription	Fetal Brain Male	brain
30	chr5:112160600-112176200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:112160800-112168400	Strong transcription	Adipose Nuclei	Adipose
32	chr5:112160800-112168600	Strong transcription	Dnd41	blood
33	chr5:112160800-112168800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112162000-112172800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:112162000-112175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:112162400-112167800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:112162400-112168800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:112162400-112171000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:112162600-112168000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:112162600-112174600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:112162800-112167600	Strong transcription	Primary B cells from cord blood	blood
42	chr5:112162800-112168400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:112162800-112168800	Strong transcription	Fetal Brain Female	brain
44	chr5:112162800-112169800	Strong transcription	Brain Hippocampus Middle	brain
45	chr5:112162800-112170000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:112162800-112170200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:112162800-112171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:112163000-112167400	Strong transcription	HSMM	muscle
49	chr5:112163000-112168400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr5:112163400-112170200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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