Variant report

Variant	rs9525095
Chromosome Location	chr13:96600508-96600509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1980942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1996054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2389530	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs2774113	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs3099358	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3099359	0.82[ASW][hapmap];0.81[YRI][hapmap]
rs3099360	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]
rs473930	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs4773927	0.91[ASW][hapmap];0.84[CEU][hapmap];0.84[TSI][hapmap]
rs4773930	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs493109	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[YRI][hapmap]
rs509572	0.81[CEU][hapmap]
rs521235	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs527680	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs529306	0.88[CEU][hapmap];0.91[CHB][hapmap]
rs539604	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs541811	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs544080	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs576184	0.82[ASW][hapmap];0.80[CEU][hapmap];0.81[YRI][hapmap]
rs595696	0.81[CEU][hapmap]
rs6492820	0.83[TSI][hapmap]
rs6492826	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7333045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7994626	0.81[CEU][hapmap]
rs7998903	0.84[CEU][hapmap];0.81[YRI][hapmap]
rs816139	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9516620	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs9525085	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];0.90[JPT][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv1597439	chr13:96600507-96600509	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9525095	MIR17HG	cis	parietal	SCAN
rs9525095	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs9525095	DZIP1	cis	parietal	SCAN
rs9525095	DZIP1	cis	cerebellum	SCAN
rs9525095	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96577000-96623200	Weak transcription	NHLF	lung
2	chr13:96577800-96608800	Weak transcription	NHEK	skin
3	chr13:96584200-96611000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:96586000-96601200	Weak transcription	NHDF-Ad	bronchial
5	chr13:96586600-96601400	Weak transcription	HUVEC	blood vessel
6	chr13:96588600-96603400	Weak transcription	NH-A	brain
7	chr13:96588800-96605400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr13:96588800-96606400	Weak transcription	Fetal Heart	heart
9	chr13:96588800-96611200	Weak transcription	Gastric	stomach
10	chr13:96589000-96601000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:96589000-96601000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr13:96589000-96601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:96589000-96602200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:96589000-96602200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:96589000-96602200	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:96589000-96602600	Weak transcription	Brain Anterior Caudate	brain
17	chr13:96589000-96603000	Weak transcription	Fetal Kidney	kidney
18	chr13:96589000-96603600	Weak transcription	Right Ventricle	heart
19	chr13:96589000-96604400	Weak transcription	Placenta	Placenta
20	chr13:96589000-96605800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr13:96589000-96609600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:96589000-96609600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:96589000-96611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:96589000-96611000	Weak transcription	Pancreas	Pancrea
25	chr13:96589000-96611800	Weak transcription	A549	lung
26	chr13:96589000-96611800	Weak transcription	HepG2	liver
27	chr13:96589000-96612000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr13:96589000-96615600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:96589200-96601000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr13:96589200-96602200	Weak transcription	Fetal Intestine Small	intestine
31	chr13:96589200-96609600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:96589200-96609600	Weak transcription	Fetal Stomach	stomach
33	chr13:96589400-96608600	Weak transcription	Brain Germinal Matrix	brain
34	chr13:96590800-96600600	Weak transcription	Fetal Brain Female	brain
35	chr13:96591400-96605800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr13:96591400-96609200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:96591600-96602200	Weak transcription	Lung	lung
38	chr13:96591600-96603600	Weak transcription	Fetal Lung	lung
39	chr13:96591600-96603600	Weak transcription	Fetal Muscle Leg	muscle
40	chr13:96591600-96605000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr13:96591600-96608400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:96591600-96608800	Weak transcription	K562	blood
43	chr13:96591600-96611000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr13:96591600-96622000	Weak transcription	Hela-S3	cervix
45	chr13:96591800-96602200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr13:96592200-96601000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:96592200-96601000	Weak transcription	Adipose Nuclei	Adipose
48	chr13:96592200-96602000	Weak transcription	Fetal Intestine Large	intestine
49	chr13:96592200-96602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr13:96592200-96602800	Weak transcription	Rectal Smooth Muscle	rectum

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