Variant report

Variant	rs521235
Chromosome Location	chr13:96647957-96647958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:96645821..96648157-chr13:96652865..96656450,3	K562	blood:
2	chr13:96646657..96649376-chr13:96653623..96656450,2	K562	blood:
3	chr13:96638885..96641405-chr13:96646337..96648047,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1980942	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1996054	0.89[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2389530	0.80[CEU][hapmap]
rs2389531	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2774113	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2849438	0.84[EUR][1000 genomes]
rs3099359	0.81[YRI][hapmap]
rs3099360	0.84[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs472788	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs473930	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4773930	0.86[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs481927	0.81[EUR][1000 genomes]
rs489179	0.81[EUR][1000 genomes]
rs493109	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506474	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs509572	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs511029	0.82[EUR][1000 genomes]
rs517173	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs527680	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs529306	0.96[CEU][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs531090	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs532399	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs536606	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs537571	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs539604	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs541811	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs544080	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs551457	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs552598	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555221	0.81[EUR][1000 genomes]
rs561996	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs566894	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs576184	0.88[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs590758	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592205	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs595696	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6492826	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7333045	0.89[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7992824	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs816139	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs816143	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9516620	0.81[YRI][hapmap]
rs9516626	0.90[EUR][1000 genomes]
rs9525081	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9525085	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9525086	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9525093	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9525095	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9525098	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9561979	0.86[EUR][1000 genomes]
rs9742440	0.83[AFR][1000 genomes];0.88[EUR][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	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	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
3	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
4	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
5	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
6	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
7	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
rs521235	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96612200-96655000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:96612200-96668600	Weak transcription	Pancreas	Pancrea
3	chr13:96613200-96694200	Weak transcription	A549	lung
4	chr13:96613600-96650000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:96613600-96663600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:96614000-96652400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:96616200-96668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:96616800-96668400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:96617000-96649000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:96617000-96663200	Weak transcription	NHDF-Ad	bronchial
11	chr13:96618800-96654200	Weak transcription	Fetal Lung	lung
12	chr13:96621600-96668600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:96622000-96668600	Weak transcription	Aorta	Aorta
14	chr13:96622200-96660400	Weak transcription	Ovary	ovary
15	chr13:96622200-96668600	Weak transcription	Fetal Kidney	kidney
16	chr13:96622200-96671400	Weak transcription	Hela-S3	cervix
17	chr13:96622200-96677200	Weak transcription	NH-A	brain
18	chr13:96622400-96668200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:96623600-96668200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:96630200-96660400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:96632400-96657600	Weak transcription	GM12878-XiMat	blood
22	chr13:96632800-96657800	Weak transcription	Fetal Muscle Leg	muscle
23	chr13:96634800-96668200	Weak transcription	Fetal Stomach	stomach
24	chr13:96635600-96657400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:96635600-96657600	Weak transcription	Left Ventricle	heart
26	chr13:96635600-96659200	Weak transcription	Adipose Nuclei	Adipose
27	chr13:96635800-96655200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:96636000-96650400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:96636400-96659000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:96640200-96651800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr13:96640400-96650200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:96640400-96650600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr13:96640400-96655800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr13:96640600-96650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr13:96640800-96648000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr13:96640800-96650000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr13:96643600-96657600	Weak transcription	Gastric	stomach
38	chr13:96645400-96659000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:96646000-96648000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:96646800-96659400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:96647200-96650400	Weak transcription	Osteobl	bone
42	chr13:96647400-96659200	Weak transcription	Psoas Muscle	Psoas
43	chr13:96647600-96648200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:96647600-96668200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr13:96647800-96648400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:96647800-96648600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:96647800-96651000	Strong transcription	HSMM	muscle

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