Variant report

Variant	rs6540564
Chromosome Location	chr1:210019910-210019911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210017330..210020093-chr1:210023208..210026466,3	K562	blood:
2	chr1:210013064..210016584-chr1:210019890..210022757,3	MCF-7	breast:
3	chr1:210018303..210020361-chr1:210546029..210548987,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1073150	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11803382	0.90[ASN][1000 genomes]
rs11805830	0.90[ASN][1000 genomes]
rs1319072	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1319435	0.87[EUR][1000 genomes]
rs1415543	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17015218	0.88[ASN][1000 genomes]
rs17015224	0.88[ASN][1000 genomes]
rs17015226	0.88[ASN][1000 genomes]
rs17015309	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015330	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015361	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17015379	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17317411	0.83[EUR][1000 genomes]
rs2205984	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2206043	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2357230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35508116	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753518	0.85[ASN][1000 genomes]
rs41305104	0.82[EUR][1000 genomes]
rs4556361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57315825	0.84[EUR][1000 genomes]
rs58637469	0.88[ASN][1000 genomes]
rs59100111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59435160	0.84[EUR][1000 genomes]
rs60326345	0.84[EUR][1000 genomes]
rs61747285	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540560	0.90[ASN][1000 genomes]
rs6540561	0.90[ASN][1000 genomes]
rs6540563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694552	0.85[ASN][1000 genomes]
rs6698154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73093853	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs735693	0.84[EUR][1000 genomes]
rs735694	0.88[EUR][1000 genomes]
rs7511996	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7522045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525951	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7539638	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540237	0.87[EUR][1000 genomes]
rs7550857	0.88[ASN][1000 genomes]
rs7551944	0.88[EUR][1000 genomes]
rs926346	0.88[ASN][1000 genomes]
rs926347	0.88[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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
2	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:210004000-210027600	Strong transcription	K562	blood
16	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
19	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
21	chr1:210004200-210020200	Strong transcription	Brain Angular Gyrus	brain
22	chr1:210004200-210020200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:210004200-210022000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
33	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
35	chr1:210004400-210029400	Strong transcription	Dnd41	blood
36	chr1:210004600-210028000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:210004600-210028000	Strong transcription	GM12878-XiMat	blood
38	chr1:210005400-210020000	Strong transcription	Rectal Smooth Muscle	rectum
39	chr1:210006200-210025400	Strong transcription	Brain Hippocampus Middle	brain
40	chr1:210006600-210020400	Strong transcription	Ovary	ovary
41	chr1:210010200-210020000	Strong transcription	Esophagus	oesophagus
42	chr1:210010200-210020000	Strong transcription	Spleen	Spleen
43	chr1:210010200-210020400	Strong transcription	Fetal Stomach	stomach
44	chr1:210010400-210020000	Strong transcription	Aorta	Aorta
45	chr1:210012000-210020800	Strong transcription	HepG2	liver
46	chr1:210013200-210028800	Strong transcription	Fetal Intestine Large	intestine
47	chr1:210013400-210028800	Strong transcription	Liver	Liver
48	chr1:210013800-210022200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:210013800-210028000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:210013800-210029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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