Variant report

Variant	rs555221
Chromosome Location	chr13:96683574-96683575
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1807900	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2389530	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34482628	0.86[EUR][1000 genomes]
rs472788	0.82[EUR][1000 genomes]
rs473930	0.82[EUR][1000 genomes]
rs481927	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs485648	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs489179	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs506474	0.80[EUR][1000 genomes]
rs509572	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs511029	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs517173	0.81[EUR][1000 genomes]
rs521235	0.81[EUR][1000 genomes]
rs527096	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531090	0.80[EUR][1000 genomes]
rs532399	0.80[EUR][1000 genomes]
rs535812	0.82[EUR][1000 genomes]
rs536606	0.80[EUR][1000 genomes]
rs541811	0.82[EUR][1000 genomes]
rs544080	0.82[EUR][1000 genomes]
rs551457	0.82[EUR][1000 genomes]
rs552598	0.83[EUR][1000 genomes]
rs561996	0.81[EUR][1000 genomes]
rs576184	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs590758	0.81[EUR][1000 genomes]
rs592205	0.80[EUR][1000 genomes]
rs595696	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516620	0.81[EUR][1000 genomes]
rs9516629	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9525091	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv530390	chr13:96681439-97193029	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs555221	UGGT2	cis	Muscle Skeletal	GTEx
rs555221	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
3	chr13:96663200-96685400	Weak transcription	HMEC	breast
4	chr13:96664200-96684800	Weak transcription	NHLF	lung
5	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr13:96668800-96685400	Weak transcription	Gastric	stomach
7	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:96669000-96686200	Weak transcription	NHEK	skin
9	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
10	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:96669400-96685400	Weak transcription	Fetal Kidney	kidney
12	chr13:96669400-96685600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:96669400-96685600	Weak transcription	Fetal Brain Female	brain
14	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
16	chr13:96669600-96686400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:96669600-96686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr13:96669600-96687000	Weak transcription	Adipose Nuclei	Adipose
19	chr13:96669800-96685600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:96669800-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:96669800-96686400	Weak transcription	Fetal Lung	lung
22	chr13:96670400-96685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:96672400-96685600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:96672800-96684000	Weak transcription	K562	blood
25	chr13:96673000-96685000	Weak transcription	GM12878-XiMat	blood
26	chr13:96673000-96685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:96673000-96698400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:96673200-96684600	Weak transcription	Hela-S3	cervix
29	chr13:96673200-96686000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:96673200-96686400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:96673200-96692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:96673200-96693400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr13:96673400-96686000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:96673400-96686000	Weak transcription	Fetal Muscle Leg	muscle
35	chr13:96673400-96686400	Weak transcription	Liver	Liver
36	chr13:96673400-96693000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr13:96673600-96685400	Weak transcription	Pancreas	Pancrea
38	chr13:96673600-96685600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr13:96673600-96685600	Weak transcription	Fetal Intestine Small	intestine
40	chr13:96673600-96686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:96673600-96686800	Weak transcription	Left Ventricle	heart
42	chr13:96674200-96685800	Weak transcription	Fetal Intestine Large	intestine
43	chr13:96676800-96683600	Weak transcription	Small Intestine	intestine
44	chr13:96677400-96685600	Weak transcription	Fetal Stomach	stomach
45	chr13:96677400-96685600	Weak transcription	Lung	lung
46	chr13:96677400-96686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:96677400-96686600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr13:96677400-96693800	Weak transcription	Aorta	Aorta
49	chr13:96677600-96685800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:96677600-96686800	Weak transcription	H1 Cell Line	embryonic stem cell

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