Variant report

Variant	rs66476638
Chromosome Location	chr2:64203143-64203144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr2:64203102-64203714	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64203137..64204872-chr2:64208577..64210562,2	K562	blood:
2	chr2:64198229..64200960-chr2:64202925..64205007,3	K562	blood:

Variant related genes	Relation type
VPS54	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10166971	0.86[ASN][1000 genomes]
rs10190776	0.84[ASN][1000 genomes]
rs12463827	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12466966	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468093	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12474366	0.82[EUR][1000 genomes]
rs12475294	0.94[EUR][1000 genomes]
rs12988017	0.87[EUR][1000 genomes]
rs12990604	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993544	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12996147	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12997303	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12999675	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13005218	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13007342	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007731	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13009774	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010817	0.90[EUR][1000 genomes]
rs13014781	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13015703	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13023542	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13025640	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028805	0.88[EUR][1000 genomes]
rs13034260	0.93[EUR][1000 genomes]
rs1345479	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1437455	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545196	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17555655	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17562312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17620012	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17701685	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17701709	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17752683	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2002443	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2119133	0.81[ASN][1000 genomes]
rs2287361	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2422110	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34043307	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34145077	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34196086	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34200806	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34239752	0.87[EUR][1000 genomes]
rs34512058	0.93[EUR][1000 genomes]
rs34683043	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34700615	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35058898	0.87[EUR][1000 genomes]
rs35122209	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35247801	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35521527	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35552326	0.87[EUR][1000 genomes]
rs35648996	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35693031	0.93[ASN][1000 genomes]
rs35810427	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35939512	0.81[EUR][1000 genomes]
rs35972278	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35975566	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36085609	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36099158	0.87[EUR][1000 genomes]
rs3815616	0.95[EUR][1000 genomes]
rs3934536	0.92[EUR][1000 genomes]
rs4075010	0.83[EUR][1000 genomes]
rs4482470	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4485552	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4544421	0.93[EUR][1000 genomes]
rs4599090	0.93[EUR][1000 genomes]
rs4671072	0.90[EUR][1000 genomes]
rs4671537	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671538	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4671540	0.87[ASN][1000 genomes]
rs4671541	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66535980	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66595136	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66650505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66660401	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66993685	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67366434	0.88[EUR][1000 genomes]
rs6759803	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67962955	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71422402	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72808216	0.84[EUR][1000 genomes]
rs72808218	0.82[EUR][1000 genomes]
rs72808231	0.94[EUR][1000 genomes]
rs72808248	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808254	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808262	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808287	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs874695	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs893779	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002209	chr2:64160385-64238475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
2	chr2:64130400-64211200	Weak transcription	Fetal Brain Male	brain
3	chr2:64137400-64204800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:64139800-64220600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:64154800-64242600	Weak transcription	Aorta	Aorta
6	chr2:64159600-64211600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:64163200-64207600	Weak transcription	HUVEC	blood vessel
8	chr2:64168800-64204800	Weak transcription	Psoas Muscle	Psoas
9	chr2:64169000-64215000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:64175600-64213000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:64176000-64204600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:64176000-64228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:64176200-64205400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:64176400-64205000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:64177600-64204600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:64177600-64212600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:64178200-64211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:64183800-64204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:64184000-64205200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:64185600-64203800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:64185800-64245000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:64186800-64216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:64187600-64203200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:64187600-64210200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:64187600-64211400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:64187800-64210200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:64187800-64211200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:64188000-64210000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:64189600-64204800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:64189800-64204800	Weak transcription	A549	lung
31	chr2:64189800-64205000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:64190000-64205200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:64190000-64212000	Weak transcription	Stomach Mucosa	stomach
34	chr2:64190000-64212800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:64190800-64203800	Strong transcription	Liver	Liver
36	chr2:64192000-64204600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:64192400-64207600	Strong transcription	HepG2	liver
38	chr2:64194000-64243200	Weak transcription	NHLF	lung
39	chr2:64196200-64205600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:64196400-64212400	Weak transcription	Colonic Mucosa	Colon
41	chr2:64196600-64205000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:64197000-64204600	Weak transcription	GM12878-XiMat	blood
43	chr2:64197600-64209200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:64197800-64203200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:64198200-64204800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:64198400-64209800	Weak transcription	Brain Hippocampus Middle	brain
47	chr2:64198400-64210000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:64198400-64211400	Weak transcription	NH-A	brain
49	chr2:64198400-64211800	Weak transcription	HSMMtube	muscle
50	chr2:64198400-64213400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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