Variant report

Variant	rs590758
Chromosome Location	chr13:96668927-96668928
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:96668658-96669297	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
UGGT2	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1980942	0.86[EUR][1000 genomes]
rs1996054	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389531	0.81[EUR][1000 genomes]
rs2774113	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2849438	0.83[EUR][1000 genomes]
rs472788	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs473930	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481927	0.81[EUR][1000 genomes]
rs489179	0.81[EUR][1000 genomes]
rs493109	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs506474	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs509572	0.83[EUR][1000 genomes]
rs511029	0.81[EUR][1000 genomes]
rs517173	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs521235	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs527680	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs529306	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs531090	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs532399	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs536606	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537571	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs539604	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs541811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544080	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552598	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs555221	0.81[EUR][1000 genomes]
rs561996	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs566894	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs576184	0.80[EUR][1000 genomes]
rs592205	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs595696	0.83[EUR][1000 genomes]
rs6492826	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7333045	0.81[EUR][1000 genomes]
rs7992824	0.82[EUR][1000 genomes]
rs816139	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs816143	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9516626	0.90[EUR][1000 genomes]
rs9525081	0.85[EUR][1000 genomes]
rs9525085	0.84[EUR][1000 genomes]
rs9525086	0.86[EUR][1000 genomes]
rs9525093	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9525098	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9561979	0.84[EUR][1000 genomes]
rs9742440	0.86[EUR][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	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590758	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
3	chr13:96622200-96677200	Weak transcription	NH-A	brain
4	chr13:96651000-96671800	Weak transcription	HSMM	muscle
5	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
6	chr13:96659400-96672600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:96660400-96678600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr13:96660600-96676600	Weak transcription	Osteobl	bone
10	chr13:96660800-96672600	Weak transcription	Liver	Liver
11	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
12	chr13:96661200-96669200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:96663200-96685400	Weak transcription	HMEC	breast
14	chr13:96663800-96672600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr13:96664000-96677200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr13:96664200-96677600	Weak transcription	NHDF-Ad	bronchial
17	chr13:96664200-96684800	Weak transcription	NHLF	lung
18	chr13:96665200-96669200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:96667200-96672200	Weak transcription	Brain Hippocampus Middle	brain
20	chr13:96668000-96669000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
21	chr13:96668000-96669000	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr13:96668000-96669000	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr13:96668000-96669200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:96668000-96669400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr13:96668000-96669400	ZNF genes & repeats	Fetal Lung	lung
26	chr13:96668000-96669800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
27	chr13:96668000-96669800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr13:96668000-96669800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr13:96668000-96670000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr13:96668000-96670000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr13:96668000-96670400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:96668200-96669200	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr13:96668200-96669200	ZNF genes & repeats	Fetal Stomach	stomach
34	chr13:96668200-96669400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:96668200-96669400	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr13:96668200-96669400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr13:96668200-96669400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
38	chr13:96668200-96669600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
39	chr13:96668200-96669600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:96668200-96669800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:96668200-96669800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
42	chr13:96668200-96669800	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr13:96668200-96669800	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr13:96668400-96669000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:96668400-96669200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:96668400-96669200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr13:96668400-96669200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
48	chr13:96668400-96669400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:96668400-96669400	ZNF genes & repeats	Fetal Brain Female	brain
50	chr13:96668400-96669600	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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