Variant report

Variant	rs6546043
Chromosome Location	chr2:64207445-64207446
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64205616..64208065-chr2:64244741..64246328,2	K562	blood:

Variant related genes	Relation type
ENSG00000143952	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10171008	0.86[ASN][1000 genomes]
rs10187013	0.82[CEU][hapmap]
rs10201844	0.82[CEU][hapmap];0.84[CHB][hapmap]
rs10207847	0.81[ASN][1000 genomes]
rs11125986	0.80[ASN][1000 genomes]
rs11682249	0.81[CHB][hapmap]
rs12611543	0.84[ASN][1000 genomes]
rs12612549	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12615049	0.84[ASN][1000 genomes]
rs1362797	0.80[ASN][1000 genomes]
rs1440004	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2080649	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2164735	0.85[ASN][1000 genomes]
rs2165210	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2302809	0.81[ASN][1000 genomes]
rs2901636	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs329477	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs329480	0.84[CHB][hapmap]
rs329483	0.85[ASN][1000 genomes]
rs329486	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3980405	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4072113	0.82[CEU][hapmap]
rs6546038	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6546039	0.82[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs6546042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546046	0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6705192	0.81[ASN][1000 genomes]
rs6716322	0.85[ASN][1000 genomes]
rs6724024	0.88[ASN][1000 genomes]
rs6727120	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6736556	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737855	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs6757168	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7420396	0.86[ASN][1000 genomes]
rs7560265	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7589241	0.82[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7596262	0.83[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7602952	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7608885	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3340648	chr2:64206963-64207495	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Clozapine-induced agranulocytosis	25187353	GWAS catalog

Chromatin state (count:117 , 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	chr2:64139800-64220600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:64154800-64242600	Weak transcription	Aorta	Aorta
5	chr2:64159600-64211600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:64163200-64207600	Weak transcription	HUVEC	blood vessel
7	chr2:64169000-64215000	Weak transcription	Brain Angular Gyrus	brain
8	chr2:64175600-64213000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:64176000-64228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:64177600-64212600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:64178200-64211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:64185800-64245000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:64186800-64216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:64187600-64210200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:64187600-64211400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:64187800-64210200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:64187800-64211200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:64188000-64210000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:64190000-64212000	Weak transcription	Stomach Mucosa	stomach
20	chr2:64190000-64212800	Weak transcription	Brain Substantia Nigra	brain
21	chr2:64192400-64207600	Strong transcription	HepG2	liver
22	chr2:64194000-64243200	Weak transcription	NHLF	lung
23	chr2:64196400-64212400	Weak transcription	Colonic Mucosa	Colon
24	chr2:64197600-64209200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:64198400-64209800	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:64198400-64210000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:64198400-64211400	Weak transcription	NH-A	brain
28	chr2:64198400-64211800	Weak transcription	HSMMtube	muscle
29	chr2:64198400-64213400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:64198600-64212600	Weak transcription	Fetal Heart	heart
31	chr2:64198600-64228000	Weak transcription	Right Ventricle	heart
32	chr2:64198800-64212200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:64199000-64212200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:64199000-64212800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:64199800-64208400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:64200000-64208400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:64201400-64211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:64201800-64209000	Weak transcription	Hela-S3	cervix
39	chr2:64202200-64210200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:64202800-64208600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:64202800-64232400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:64203200-64212600	Weak transcription	K562	blood
43	chr2:64203200-64228400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:64203400-64207600	Weak transcription	Fetal Intestine Large	intestine
45	chr2:64203400-64208400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:64203400-64208600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:64203400-64209400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:64203400-64211400	Weak transcription	Fetal Brain Female	brain
49	chr2:64203400-64212200	Weak transcription	Esophagus	oesophagus
50	chr2:64203400-64212200	Weak transcription	Lung	lung

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