Variant report

Variant	rs599166
Chromosome Location	chr5:15547076-15547077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:15542930..15547234-chr5:15550922..15554714,4	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11955129	1.00[AMR][1000 genomes]
rs304540	1.00[AMR][1000 genomes]
rs304553	1.00[AMR][1000 genomes]
rs304585	1.00[AMR][1000 genomes]
rs304588	1.00[AMR][1000 genomes]
rs524928	1.00[AMR][1000 genomes]
rs566631	1.00[AMR][1000 genomes]
rs590066	1.00[AMR][1000 genomes]
rs592200	1.00[AMR][1000 genomes]
rs626130	1.00[AMR][1000 genomes]
rs641200	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs644859	1.00[AMR][1000 genomes]
rs6554879	1.00[AMR][1000 genomes]
rs6554881	1.00[AMR][1000 genomes]
rs667260	1.00[AMR][1000 genomes]
rs670272	1.00[AMR][1000 genomes]
rs676820	1.00[AMR][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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs599166	ST8SIA1	trans	lymphoblastoid	seeQTL
rs599166	RNF128	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15512200-15571200	Weak transcription	HUVEC	blood vessel
2	chr5:15518800-15547400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:15524000-15558600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:15533800-15547400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:15534200-15550200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:15534400-15550600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:15536400-15561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:15536600-15547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:15539000-15547400	Weak transcription	Fetal Stomach	stomach
10	chr5:15539400-15547600	Weak transcription	Brain Substantia Nigra	brain
11	chr5:15539600-15547600	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:15539600-15549800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:15539800-15547200	Weak transcription	Fetal Muscle Leg	muscle
14	chr5:15539800-15551200	Weak transcription	Fetal Brain Female	brain
15	chr5:15540600-15555000	Weak transcription	HSMMtube	muscle
16	chr5:15540800-15554600	Weak transcription	HSMM	muscle
17	chr5:15541000-15558600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:15541400-15550800	Weak transcription	Fetal Brain Male	brain
19	chr5:15544000-15547200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:15544000-15548000	Weak transcription	Brain Angular Gyrus	brain
21	chr5:15544000-15550400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:15544200-15549200	Weak transcription	Brain Germinal Matrix	brain
23	chr5:15544200-15550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:15544400-15549800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:15544400-15550000	Weak transcription	Esophagus	oesophagus
26	chr5:15544600-15547200	Weak transcription	Right Ventricle	heart
27	chr5:15544600-15563400	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:15544800-15547800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:15544800-15549000	Weak transcription	Aorta	Aorta
30	chr5:15545000-15547200	Weak transcription	Right Atrium	heart
31	chr5:15545000-15547400	Weak transcription	Ovary	ovary
32	chr5:15545000-15547800	Weak transcription	Fetal Intestine Large	intestine
33	chr5:15545000-15549800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:15545000-15549800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:15545000-15549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:15545000-15550000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:15545000-15550800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:15545000-15550800	Weak transcription	Brain Anterior Caudate	brain
39	chr5:15545200-15549000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:15545200-15550000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:15545200-15557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:15545400-15547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:15545400-15550200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:15546600-15547800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr5:15546800-15547600	Genic enhancers	Fetal Heart	heart
46	chr5:15547000-15547600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr5:15547000-15548000	Enhancers	H9 Cell Line	embryonic stem cell
48	chr5:15547000-15548200	Enhancers	Left Ventricle	heart
49	chr5:15547000-15548600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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