Variant report

Variant	rs5024450
Chromosome Location	chr8:87364238-87364239
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	chr8:87358214..87359951-chr8:87363594..87365378,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10088739	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10089781	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10093238	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs10093379	0.82[EUR][1000 genomes]
rs10095129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10095498	0.82[JPT][hapmap]
rs10095537	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10096168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10096443	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs10097450	0.82[JPT][hapmap]
rs10103691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10107072	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10956800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10956802	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10956803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10956853	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1142528	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11775728	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11781016	0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap]
rs11782512	0.83[EUR][1000 genomes]
rs11787036	0.91[ASN][1000 genomes]
rs11787318	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11997234	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12543856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12543887	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12544731	0.96[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12546802	0.82[JPT][hapmap]
rs12550142	0.82[JPT][hapmap]
rs12679811	0.82[JPT][hapmap]
rs13042	0.82[JPT][hapmap]
rs13249753	0.82[JPT][hapmap]
rs13251647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13267782	0.82[JPT][hapmap]
rs13269259	0.82[JPT][hapmap]
rs13281414	0.82[JPT][hapmap]
rs17608598	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17608967	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17681618	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1946940	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs2953517	0.82[JPT][hapmap]
rs2976201	0.82[JPT][hapmap]
rs3213911	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs34895735	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3883910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4285463	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4484676	0.86[JPT][hapmap]
rs4490816	0.81[JPT][hapmap]
rs4581032	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4587306	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs4961187	0.91[ASN][1000 genomes]
rs4961188	0.82[JPT][hapmap]
rs4961189	0.87[ASN][1000 genomes]
rs4961190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4961193	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs4961194	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs4961195	0.81[JPT][hapmap]
rs4961196	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5025329	0.86[JPT][hapmap]
rs55727343	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55807259	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56039487	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56096624	0.88[ASN][1000 genomes]
rs56102132	0.84[EUR][1000 genomes]
rs56122638	0.92[ASN][1000 genomes]
rs56268675	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56395805	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57326273	0.88[EUR][1000 genomes]
rs57644875	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62509414	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62509419	0.95[ASN][1000 genomes]
rs62509421	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62510798	0.84[EUR][1000 genomes]
rs6415565	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6471273	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs6471279	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6471281	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471296	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs6471309	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs6471345	0.82[EUR][1000 genomes]
rs6471352	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6471354	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6471360	0.82[JPT][hapmap]
rs6983925	0.81[JPT][hapmap]
rs6988601	0.81[EUR][1000 genomes]
rs6994005	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs6996052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6999654	0.85[JPT][hapmap]
rs7003059	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs7006017	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs7006629	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7015490	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7017706	0.82[JPT][hapmap]
rs7017716	0.82[JPT][hapmap]
rs7017719	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71503461	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7459811	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7459897	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7460028	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7460251	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs7460286	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7460439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs7461413	0.82[JPT][hapmap]
rs7461624	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs7461767	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7462727	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7465350	0.96[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs7465511	0.82[JPT][hapmap]
rs7819454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7820234	0.82[JPT][hapmap]
rs7820697	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs7823154	0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs7824469	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7825405	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7830128	0.95[ASN][1000 genomes]
rs7832493	0.82[JPT][hapmap]
rs7835743	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7837569	0.82[JPT][hapmap]
rs7838007	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7839601	0.82[JPT][hapmap]
rs7846090	0.82[JPT][hapmap]
rs9283961	0.87[ASN][1000 genomes]
rs9642913	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9942792	0.81[JPT][hapmap]
rs9942823	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3360246	chr8:87200232-87419244	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1017535	chr8:87261702-87367934	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5024450	CALB1	cis	cerebellum	SCAN
rs5024450	FAM82B	cis	cerebellum	SCAN
rs5024450	CPNE3	cis	cerebellum	SCAN
rs5024450	FAM82B	cis	parietal	SCAN
rs5024450	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs5024450	CPNE3	cis	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87355800-87405600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87356800-87403800	Weak transcription	Aorta	Aorta
3	chr8:87357000-87366400	Weak transcription	Fetal Lung	lung
4	chr8:87357000-87375600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:87357200-87365000	Weak transcription	Brain Substantia Nigra	brain
6	chr8:87357200-87366000	Weak transcription	Brain Hippocampus Middle	brain
7	chr8:87357200-87368800	Weak transcription	Primary B cells from cord blood	blood
8	chr8:87357200-87369600	Weak transcription	HSMM	muscle
9	chr8:87357400-87364400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr8:87357400-87364600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:87357400-87364600	Weak transcription	Lung	lung
12	chr8:87357400-87367200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:87357400-87368000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:87357400-87372600	Weak transcription	Fetal Intestine Small	intestine
15	chr8:87357400-87403400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr8:87357600-87364800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr8:87357600-87364800	Weak transcription	Fetal Muscle Leg	muscle
18	chr8:87357600-87364800	Weak transcription	K562	blood
19	chr8:87357600-87366000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:87357600-87368800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:87357600-87368800	Weak transcription	Brain Angular Gyrus	brain
22	chr8:87357600-87374600	Weak transcription	HUVEC	blood vessel
23	chr8:87357600-87382200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr8:87357800-87367400	Weak transcription	Fetal Intestine Large	intestine
25	chr8:87357800-87368600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr8:87357800-87381000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr8:87357800-87382000	Weak transcription	Placenta	Placenta
28	chr8:87357800-87383200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr8:87357800-87413600	Weak transcription	Pancreas	Pancrea
30	chr8:87358000-87366600	Weak transcription	Colonic Mucosa	Colon
31	chr8:87358000-87369000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr8:87358400-87364800	Weak transcription	A549	lung
33	chr8:87358400-87367400	Weak transcription	Hela-S3	cervix
34	chr8:87358600-87365000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr8:87358800-87366600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:87359000-87383600	Weak transcription	Dnd41	blood
37	chr8:87359800-87372600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr8:87360600-87369800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:87361600-87364400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr8:87361600-87364800	Weak transcription	Fetal Stomach	stomach
41	chr8:87361800-87369600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:87362200-87368400	Enhancers	HepG2	liver
43	chr8:87362200-87368800	Weak transcription	Adipose Nuclei	Adipose
44	chr8:87362200-87369600	Enhancers	Stomach Mucosa	stomach
45	chr8:87362400-87364600	Weak transcription	Right Ventricle	heart
46	chr8:87362400-87378200	Weak transcription	Gastric	stomach
47	chr8:87362600-87364400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr8:87362600-87366000	Enhancers	Small Intestine	intestine
49	chr8:87362800-87364400	Enhancers	Colon Smooth Muscle	Colon
50	chr8:87363000-87366200	Enhancers	Liver	Liver

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