Variant report

Variant	rs9525085
Chromosome Location	chr13:96578933-96578934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1807900	0.83[EUR][1000 genomes]
rs1980942	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1996054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389530	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs2389531	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2774113	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099358	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs3099359	0.90[ASW][hapmap];0.81[YRI][hapmap]
rs3099360	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]
rs3125438	0.81[EUR][1000 genomes]
rs34482628	0.84[EUR][1000 genomes]
rs472788	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs473930	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4773927	0.81[ASW][hapmap];0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4773930	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs493109	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs506474	0.84[EUR][1000 genomes]
rs509572	0.81[CEU][hapmap]
rs517173	0.83[EUR][1000 genomes]
rs521235	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]
rs527680	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs529306	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs531090	0.84[EUR][1000 genomes]
rs532399	0.84[EUR][1000 genomes]
rs536606	0.84[EUR][1000 genomes]
rs539604	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs541811	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs544080	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs551457	0.85[EUR][1000 genomes]
rs552598	0.84[EUR][1000 genomes]
rs561996	0.83[EUR][1000 genomes]
rs566894	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs576184	0.90[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap]
rs590758	0.84[EUR][1000 genomes]
rs592205	0.84[EUR][1000 genomes]
rs595696	0.81[CEU][hapmap]
rs6492820	0.83[TSI][hapmap]
rs6492826	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7333045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7992824	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7994626	0.81[CEU][hapmap]
rs7998903	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs816139	0.91[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816143	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9516620	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs9516626	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9525081	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9525086	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9525091	0.82[EUR][1000 genomes]
rs9525093	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9525095	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9525098	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561979	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9742440	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	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	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
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9525085	MIR17HG	cis	parietal	SCAN
rs9525085	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs9525085	DZIP1	cis	parietal	SCAN
rs9525085	DZIP1	cis	cerebellum	SCAN
rs9525085	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:96542400-96581600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr13:96543000-96581600	Weak transcription	Fetal Lung	lung
7	chr13:96543000-96581800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
10	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
11	chr13:96558600-96579000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:96559600-96580800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr13:96559600-96583000	Weak transcription	Pancreas	Pancrea
14	chr13:96559600-96586400	Weak transcription	A549	lung
15	chr13:96559800-96580600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:96559800-96580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:96559800-96583400	Weak transcription	Esophagus	oesophagus
18	chr13:96559800-96588600	Weak transcription	Gastric	stomach
19	chr13:96560000-96581400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:96560000-96581600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:96560200-96581000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:96562600-96580600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:96566400-96581600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:96566800-96587000	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:96567600-96581600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:96568400-96579600	Weak transcription	GM12878-XiMat	blood
27	chr13:96568400-96580600	Weak transcription	Fetal Intestine Large	intestine
28	chr13:96568400-96581600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr13:96568600-96580600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr13:96568600-96580600	Weak transcription	Fetal Stomach	stomach
31	chr13:96568600-96580800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:96568600-96581600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:96568600-96582000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr13:96568600-96582800	Weak transcription	Left Ventricle	heart
35	chr13:96568600-96583000	Weak transcription	Ovary	ovary
36	chr13:96571000-96588600	Weak transcription	Psoas Muscle	Psoas
37	chr13:96574600-96581600	Weak transcription	HSMM	muscle
38	chr13:96575800-96581600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:96576200-96579000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:96576800-96579000	Enhancers	Osteobl	bone
41	chr13:96577000-96581600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr13:96577000-96581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:96577000-96623200	Weak transcription	NHLF	lung
44	chr13:96577200-96580400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:96577200-96580800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:96577200-96580800	Weak transcription	Fetal Muscle Leg	muscle
47	chr13:96577200-96581400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:96577200-96581600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr13:96577200-96581600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:96577200-96581800	Weak transcription	Fetal Heart	heart

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