Variant report

Variant	rs363092
Chromosome Location	chr4:3196029-3196030
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3195364..3197169-chr4:3200339..3201843,2	K562	blood:
2	chr4:3195267..3196266-chr4:3444903..3445887,5	MCF-7	breast:
3	chr4:3169372..3171758-chr4:3194914..3197788,2	K562	blood:
4	chr4:3187730..3190882-chr4:3194133..3197164,3	K562	blood:
5	chr4:3195952..3197606-chr4:3265003..3267231,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs110501	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16843804	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs17780797	0.89[EUR][1000 genomes]
rs1891701	0.86[ASN][1000 genomes]
rs2024115	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs2071655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2071662	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071671	0.94[JPT][hapmap]
rs2071703	0.83[ASN][1000 genomes]
rs2071704	0.88[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2157090	0.81[JPT][hapmap]
rs2237006	0.90[EUR][1000 genomes]
rs2237007	0.84[EUR][1000 genomes]
rs2269477	0.94[ASN][1000 genomes]
rs2269478	0.83[EUR][1000 genomes]
rs2269499	0.80[JPT][hapmap]
rs2285086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2298967	0.93[ASN][1000 genomes]
rs2298971	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530601	0.81[JPT][hapmap]
rs2798221	0.90[JPT][hapmap]
rs28403215	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28867436	0.85[EUR][1000 genomes]
rs3095077	0.90[JPT][hapmap]
rs3121419	0.85[JPT][hapmap]
rs3135175	0.85[ASN][1000 genomes]
rs362268	0.86[ASN][1000 genomes]
rs362271	0.80[JPT][hapmap]
rs362272	0.80[JPT][hapmap]
rs362273	0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs362275	0.93[ASN][1000 genomes]
rs362296	0.84[JPT][hapmap]
rs362306	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs362309	0.88[ASN][1000 genomes]
rs362312	0.83[ASN][1000 genomes]
rs362314	0.84[EUR][1000 genomes]
rs362319	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs362331	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs362336	0.94[ASN][1000 genomes]
rs363063	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs363064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs363066	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs363088	0.98[ASN][1000 genomes]
rs363091	0.88[MKK][hapmap]
rs363096	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs363099	0.83[ASN][1000 genomes]
rs3755883	0.91[ASN][1000 genomes]
rs3775061	0.85[ASN][1000 genomes]
rs3856973	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4690011	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs4690073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4690075	0.90[ASN][1000 genomes]
rs59613878	0.88[ASN][1000 genomes]
rs60197694	0.85[ASN][1000 genomes]
rs61792530	0.85[ASN][1000 genomes]
rs6446723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs6446727	0.81[JPT][hapmap]
rs6446731	0.81[JPT][hapmap]
rs66684864	0.93[ASN][1000 genomes]
rs6844859	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6855981	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs73193303	0.94[ASN][1000 genomes]
rs7659144	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7661630	0.81[JPT][hapmap]
rs7685686	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7691627	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs82332	0.92[ASN][1000 genomes]
rs82333	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs82334	0.92[ASN][1000 genomes]
rs916171	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9996868	0.81[JPT][hapmap]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs363092	OTOP1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
8	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr4:3176400-3199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:3178800-3200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:3181000-3201400	Weak transcription	Hela-S3	cervix
18	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:3182400-3203200	Strong transcription	Fetal Intestine Large	intestine
20	chr4:3183000-3197400	Strong transcription	Dnd41	blood
21	chr4:3183000-3202600	Strong transcription	Liver	Liver
22	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:3189200-3199800	Strong transcription	Primary B cells from cord blood	blood
25	chr4:3190600-3203600	Weak transcription	Small Intestine	intestine
26	chr4:3191200-3201400	Weak transcription	Psoas Muscle	Psoas
27	chr4:3191200-3201400	Weak transcription	NHDF-Ad	bronchial
28	chr4:3191200-3203400	Weak transcription	Fetal Heart	heart
29	chr4:3191200-3208600	Weak transcription	A549	lung
30	chr4:3191400-3196600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:3191400-3197400	Weak transcription	Colonic Mucosa	Colon
32	chr4:3191600-3196200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:3191600-3196400	Weak transcription	Fetal Brain Male	brain
34	chr4:3191600-3196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:3191600-3199200	Weak transcription	HSMMtube	muscle
36	chr4:3191600-3201400	Weak transcription	NH-A	brain
37	chr4:3191600-3203600	Weak transcription	K562	blood
38	chr4:3191800-3197400	Weak transcription	NHLF	lung
39	chr4:3191800-3197600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:3191800-3207800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:3191800-3208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr4:3191800-3211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:3192000-3196200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:3192000-3201400	Weak transcription	Colon Smooth Muscle	Colon
45	chr4:3192200-3196800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:3192200-3198600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:3192600-3197600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr4:3192600-3197600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr4:3192800-3196400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:3192800-3196400	Weak transcription	Brain Hippocampus Middle	brain

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