Variant report

Variant	rs3099360
Chromosome Location	chr13:96505952-96505953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1980942	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996054	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389530	0.81[CEU][hapmap]
rs2389531	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2774113	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs3099358	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099359	0.82[ASW][hapmap]
rs3125438	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34859372	0.81[EUR][1000 genomes]
rs473930	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4773927	0.91[ASW][hapmap];0.84[CEU][hapmap];0.81[AFR][1000 genomes]
rs4773930	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs521235	0.84[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap]
rs541811	0.91[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap]
rs544080	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs566894	0.85[ASN][1000 genomes]
rs6492826	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs7333045	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7992824	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7994626	0.81[CEU][hapmap]
rs7998903	0.84[CEU][hapmap]
rs816139	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs816143	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9516626	0.85[ASN][1000 genomes]
rs9525081	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525085	0.91[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9525086	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525093	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9525095	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs9525098	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9561979	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9742440	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3099360	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs3099360	DZIP1	cis	parietal	SCAN
rs3099360	DZIP1	cis	cerebellum	SCAN
rs3099360	UGGT2	cis	Skin Sun Exposed Lower leg	GTEx
rs3099360	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96487000-96510000	Weak transcription	HUVEC	blood vessel
3	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:96499400-96515400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:96502000-96522400	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:96502400-96535400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:96502600-96506400	Strong transcription	Fetal Intestine Large	intestine
9	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
10	chr13:96502800-96506600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:96502800-96506800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:96502800-96514800	Weak transcription	Gastric	stomach
13	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:96503000-96506000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:96503000-96506200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:96503000-96506600	Strong transcription	HSMM	muscle
17	chr13:96503000-96506800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:96503000-96506800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:96503000-96508600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:96503000-96510600	Weak transcription	NHLF	lung
21	chr13:96503000-96517400	Weak transcription	K562	blood
22	chr13:96503000-96522600	Weak transcription	Aorta	Aorta
23	chr13:96503000-96522600	Weak transcription	Pancreas	Pancrea
24	chr13:96503000-96523600	Weak transcription	Esophagus	oesophagus
25	chr13:96503000-96526800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:96503000-96527200	Weak transcription	Fetal Kidney	kidney
27	chr13:96503000-96567400	Weak transcription	NHEK	skin
28	chr13:96503200-96506200	Weak transcription	Right Ventricle	heart
29	chr13:96503200-96506800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr13:96503200-96508200	Weak transcription	Brain Anterior Caudate	brain
31	chr13:96503200-96510200	Weak transcription	Hela-S3	cervix
32	chr13:96503200-96510400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr13:96503200-96522600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:96503200-96522800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr13:96503200-96527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr13:96503200-96535200	Weak transcription	HepG2	liver
37	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
38	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
40	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
41	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr13:96503400-96506200	Weak transcription	GM12878-XiMat	blood
44	chr13:96503400-96520400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:96503400-96521800	Weak transcription	HSMMtube	muscle
46	chr13:96503400-96522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr13:96503400-96528600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
50	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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