Variant report

Variant	rs9516620
Chromosome Location	chr13:96538424-96538425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1596710	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs1807900	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1980942	0.88[CEU][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs1996054	0.89[CEU][hapmap]
rs2389530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389531	0.87[EUR][1000 genomes]
rs3099357	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs3099359	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3125433	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34482628	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34859372	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs473930	0.86[YRI][hapmap]
rs4773927	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773930	0.85[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs481927	0.81[EUR][1000 genomes]
rs489179	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs493109	0.86[YRI][hapmap]
rs509572	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs511029	0.81[EUR][1000 genomes]
rs521235	0.81[YRI][hapmap]
rs541811	0.93[YRI][hapmap]
rs544080	0.86[YRI][hapmap]
rs555221	0.81[EUR][1000 genomes]
rs576184	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs595696	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs6492820	0.88[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs6492826	0.81[YRI][hapmap]
rs7333045	0.89[CEU][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs7983756	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap]
rs7994626	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998903	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816139	0.85[YRI][hapmap]
rs9302083	0.93[JPT][hapmap]
rs9516629	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9525081	0.80[EUR][1000 genomes]
rs9525085	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs9525086	0.82[EUR][1000 genomes]
rs9525091	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9525095	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs9561930	0.94[JPT][hapmap]
rs9561949	0.85[EUR][1000 genomes]
rs9742440	0.82[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	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv519575	chr13:96537274-96540204	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9516620	UGGT2	cis	Muscle Skeletal	GTEx
rs9516620	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
5	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:96503000-96567400	Weak transcription	NHEK	skin
7	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
8	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
11	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
15	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
18	chr13:96503800-96548200	Weak transcription	A549	lung
19	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
20	chr13:96510800-96556000	Weak transcription	Psoas Muscle	Psoas
21	chr13:96511000-96559000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:96511000-96559200	Weak transcription	Spleen	Spleen
23	chr13:96515000-96553400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:96515200-96542000	Weak transcription	Gastric	stomach
25	chr13:96518200-96553200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr13:96519600-96546400	Weak transcription	Right Ventricle	heart
27	chr13:96520800-96559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr13:96522400-96542000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr13:96523000-96559000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:96523200-96547800	Weak transcription	Colon Smooth Muscle	Colon
31	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr13:96523800-96542200	Weak transcription	Fetal Brain Male	brain
33	chr13:96524000-96561200	Weak transcription	HMEC	breast
34	chr13:96524200-96542600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr13:96524200-96560400	Weak transcription	Brain Angular Gyrus	brain
36	chr13:96526400-96548200	Weak transcription	K562	blood
37	chr13:96527800-96559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:96528200-96548200	Weak transcription	HUVEC	blood vessel
39	chr13:96528200-96558600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr13:96528800-96559000	Weak transcription	Ovary	ovary
41	chr13:96529000-96550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:96529200-96552600	Weak transcription	NHLF	lung
43	chr13:96529200-96558000	Weak transcription	Fetal Kidney	kidney
44	chr13:96529400-96542000	Weak transcription	Fetal Intestine Small	intestine
45	chr13:96529400-96542000	Weak transcription	Lung	lung
46	chr13:96529400-96542400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr13:96529400-96547600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr13:96529400-96558200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr13:96529400-96559000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:96529400-96559000	Weak transcription	H9 Cell Line	embryonic stem cell

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