Variant report

Variant	rs509572
Chromosome Location	chr13:96665151-96665152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1807900	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980942	0.81[CEU][hapmap]
rs1996054	0.81[CEU][hapmap]
rs2389530	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2774113	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs3099357	1.00[ASW][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs3099359	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs34482628	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs472788	0.84[EUR][1000 genomes]
rs473930	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs4773927	0.88[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs481927	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485648	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs489179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493109	0.87[CEU][hapmap]
rs506474	0.82[EUR][1000 genomes]
rs511029	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517173	0.83[EUR][1000 genomes]
rs521235	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs527096	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527680	0.88[CEU][hapmap]
rs529306	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs531090	0.82[EUR][1000 genomes]
rs532399	0.82[EUR][1000 genomes]
rs535812	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs536606	0.82[EUR][1000 genomes]
rs539604	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs541811	0.88[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs544080	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs551457	0.84[EUR][1000 genomes]
rs552598	0.83[EUR][1000 genomes]
rs555221	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs561996	0.82[EUR][1000 genomes]
rs566894	0.80[EUR][1000 genomes]
rs576184	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs590758	0.83[EUR][1000 genomes]
rs592205	0.82[EUR][1000 genomes]
rs595696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492826	0.88[CEU][hapmap]
rs7994626	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs7998903	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs816139	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs9516620	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs9516629	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9525085	0.81[CEU][hapmap]
rs9525091	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9525095	0.81[CEU][hapmap]
rs9525098	0.86[CEU][hapmap];0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs509572	UGGT2	cis	Muscle Skeletal	GTEx
rs509572	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96612200-96668600	Weak transcription	Pancreas	Pancrea
2	chr13:96613200-96694200	Weak transcription	A549	lung
3	chr13:96616200-96668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr13:96616800-96668400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:96621600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:96622000-96668600	Weak transcription	Aorta	Aorta
7	chr13:96622200-96668600	Weak transcription	Fetal Kidney	kidney
8	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
9	chr13:96622200-96677200	Weak transcription	NH-A	brain
10	chr13:96622400-96668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:96623600-96668200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:96634800-96668200	Weak transcription	Fetal Stomach	stomach
13	chr13:96647600-96668200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr13:96648000-96668200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:96648200-96668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:96651000-96671800	Weak transcription	HSMM	muscle
17	chr13:96652600-96668400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:96652800-96668000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:96655400-96668400	Weak transcription	Fetal Brain Male	brain
20	chr13:96655600-96668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:96656000-96668000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:96656000-96668000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:96656000-96668200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:96656000-96668200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr13:96657600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:96657800-96668200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
28	chr13:96658400-96668600	Weak transcription	Left Ventricle	heart
29	chr13:96658400-96668600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:96659200-96668200	Weak transcription	Brain Germinal Matrix	brain
31	chr13:96659400-96668200	Weak transcription	Fetal Intestine Large	intestine
32	chr13:96659400-96672600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr13:96660400-96668000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr13:96660400-96668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:96660400-96678600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:96660600-96676600	Weak transcription	Osteobl	bone
38	chr13:96660800-96668600	Weak transcription	Ovary	ovary
39	chr13:96660800-96672600	Weak transcription	Liver	Liver
40	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
41	chr13:96661000-96668000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr13:96661000-96668000	Weak transcription	Fetal Lung	lung
43	chr13:96661000-96668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:96661200-96668200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:96661200-96669200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:96661400-96668000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr13:96661400-96668000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:96661400-96668400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:96661600-96668200	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:96662800-96668000	Weak transcription	Adipose Nuclei	Adipose

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