Variant report

Variant	rs6546040
Chromosome Location	chr2:64122439-64122440
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64116985..64119241-chr2:64121510..64125671,3	K562	blood:
2	chr2:64122001..64123547-chr2:64129156..64130782,2	K562	blood:
3	chr2:64118955..64120810-chr2:64121223..64123718,2	K562	blood:
4	chr2:64121804..64124503-chr2:64129282..64132356,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10171008	0.86[ASN][1000 genomes]
rs10207847	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11125986	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12611543	0.80[ASN][1000 genomes]
rs12612549	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12615049	0.80[ASN][1000 genomes]
rs1362797	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1440004	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2080649	0.84[EUR][1000 genomes]
rs2165210	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2302809	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2901636	0.83[EUR][1000 genomes]
rs329477	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs329486	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3980405	0.85[EUR][1000 genomes]
rs6546038	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546039	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546042	0.82[ASN][1000 genomes]
rs6546046	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6705192	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716322	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6716558	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6724024	0.85[ASN][1000 genomes]
rs6727120	0.80[EUR][1000 genomes]
rs6746875	0.85[EUR][1000 genomes]
rs6757168	0.87[ASN][1000 genomes]
rs7420396	0.86[ASN][1000 genomes]
rs7560265	0.82[ASN][1000 genomes]
rs7589241	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7596262	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7602952	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7608885	0.82[EUR][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	nsv521717	chr2:64104132-64186582	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:64103600-64128400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:64103800-64130400	Weak transcription	Stomach Mucosa	stomach
5	chr2:64107200-64130000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:64107400-64127600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:64107400-64129600	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:64107600-64128800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr2:64107600-64129200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:64107800-64124600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:64107800-64126200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:64107800-64127000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr2:64108200-64127200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:64108400-64127200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:64108600-64128200	Strong transcription	Primary hematopoietic stem cells	blood
16	chr2:64109200-64125800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:64109400-64127000	Strong transcription	Placenta	Placenta
18	chr2:64109400-64129000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:64109600-64122800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:64109600-64127000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:64109600-64128400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:64109800-64122800	Strong transcription	Osteobl	bone
23	chr2:64109800-64128600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:64110000-64126800	Strong transcription	Adipose Nuclei	Adipose
25	chr2:64110200-64126800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:64110200-64127000	Strong transcription	Fetal Thymus	thymus
27	chr2:64110400-64126200	Strong transcription	Primary T cells from cord blood	blood
28	chr2:64110400-64126600	Strong transcription	Dnd41	blood
29	chr2:64112600-64127000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr2:64112800-64129600	Strong transcription	NH-A	brain
31	chr2:64114000-64128800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:64114000-64129200	Weak transcription	Fetal Brain Male	brain
33	chr2:64114000-64130600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
35	chr2:64114200-64174800	Weak transcription	Right Ventricle	heart
36	chr2:64115400-64124200	Weak transcription	Fetal Kidney	kidney
37	chr2:64115800-64123000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:64115800-64129200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:64116000-64127000	Strong transcription	Liver	Liver
40	chr2:64116000-64127800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:64116000-64128000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:64116000-64128800	Weak transcription	Aorta	Aorta
43	chr2:64116000-64129200	Weak transcription	Spleen	Spleen
44	chr2:64116200-64125200	Weak transcription	Gastric	stomach
45	chr2:64116200-64127800	Weak transcription	Fetal Intestine Small	intestine
46	chr2:64116400-64126400	Weak transcription	Fetal Heart	heart
47	chr2:64116400-64129200	Weak transcription	Pancreas	Pancrea
48	chr2:64116800-64124200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:64116800-64125400	Weak transcription	Lung	lung
50	chr2:64116800-64138600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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