Variant report

Variant	rs12529549
Chromosome Location	chr6:38275246-38275247
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38269604..38272894-chr6:38272996..38276303,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10484931	0.84[ASN][1000 genomes]
rs12173290	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12524225	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12527432	0.86[ASN][1000 genomes]
rs12660323	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664994	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16890552	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16890561	0.83[ASN][1000 genomes]
rs4711531	0.85[ASN][1000 genomes]
rs4711532	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4714139	0.86[ASN][1000 genomes]
rs4714141	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4714145	0.85[ASN][1000 genomes]
rs57012325	0.94[ASN][1000 genomes]
rs57934228	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59624393	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60500173	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6938840	0.82[ASN][1000 genomes]
rs714930	0.83[ASN][1000 genomes]
rs73422824	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73422833	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73730927	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73730928	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7771835	0.82[ASN][1000 genomes]
rs871182	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs871184	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296243	0.81[ASN][1000 genomes]
rs9349065	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9366951	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9366952	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9369044	0.82[ASN][1000 genomes]
rs9369045	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9369046	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369047	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369050	0.82[ASN][1000 genomes]
rs9380728	0.86[ASN][1000 genomes]
rs9380729	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9380730	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9380731	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9380732	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9380733	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9380734	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9394483	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9394485	0.90[ASN][1000 genomes]
rs9394487	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9394490	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394491	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38249200-38275600	Weak transcription	Fetal Brain Male	brain
2	chr6:38270200-38275400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:38270800-38275600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:38271200-38275600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:38273400-38275800	Enhancers	Psoas Muscle	Psoas
6	chr6:38273400-38276200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:38273600-38276200	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:38273800-38275800	Enhancers	Fetal Muscle Leg	muscle
9	chr6:38273800-38276000	Enhancers	Primary hematopoietic stem cells	blood
10	chr6:38273800-38276000	Enhancers	Brain Hippocampus Middle	brain
11	chr6:38273800-38276000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:38273800-38276200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:38273800-38276200	Enhancers	Brain Anterior Caudate	brain
14	chr6:38273800-38276800	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:38274000-38275400	Enhancers	Right Ventricle	heart
16	chr6:38274000-38275800	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:38274000-38275800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:38274000-38276000	Enhancers	Fetal Stomach	stomach
19	chr6:38274000-38276200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:38274000-38276200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:38274000-38276200	Enhancers	Fetal Lung	lung
22	chr6:38274000-38276800	Enhancers	Dnd41	blood
23	chr6:38274200-38275800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:38274200-38276000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr6:38274200-38276200	Enhancers	Primary B cells from cord blood	blood
26	chr6:38274200-38276200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:38274200-38276200	Enhancers	HSMMtube	muscle
28	chr6:38274400-38275600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:38274400-38275600	Enhancers	HSMM	muscle
30	chr6:38274400-38276000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:38274400-38276200	Enhancers	Fetal Heart	heart
32	chr6:38274400-38276200	Enhancers	Fetal Kidney	kidney
33	chr6:38274400-38288600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:38274600-38276000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:38274600-38276000	Enhancers	Primary T cells from cord blood	blood
36	chr6:38274600-38276000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr6:38274600-38276200	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr6:38274600-38276800	Enhancers	Fetal Thymus	thymus
39	chr6:38274800-38275800	Weak transcription	NHDF-Ad	bronchial
40	chr6:38275000-38276000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr6:38275000-38277800	Weak transcription	Right Atrium	heart
42	chr6:38275200-38275400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:38275200-38275600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:38275200-38276000	Enhancers	Thymus	Thymus

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