Variant report

Variant	rs3856973
Chromosome Location	chr4:3080173-3080174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3079518-3080557	GM12892	blood:	n/a	n/a
2	ZNF143	chr4:3079611-3080220	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:3079346-3080607	GM12878	blood:	n/a	n/a
5	PML	chr4:3079399-3080280	GM12878	blood:	n/a	n/a
6	NFIC	chr4:3078814-3080343	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:3079450-3080187	GM12878	blood:	n/a	n/a
8	EP300	chr4:3079474-3080180	GM12878	blood:	n/a	chr4:3079699-3079713
9	STAT3	chr4:3079513-3080448	GM12878	blood:	n/a	n/a
10	USF2	chr4:3079525-3080219	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:3080050-3080178	MCF10A-Er-Src	breast:	n/a	n/a
12	RCOR1	chr4:3079562-3080177	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:3080145-3080561	GM12892	blood:	n/a	n/a
14	CHD1	chr4:3079453-3080274	GM12878	blood:	n/a	n/a
15	FOXM1	chr4:3079318-3080213	GM12878	blood:	n/a	n/a
16	NFIC	chr4:3079342-3080185	GM12878	blood:	n/a	n/a
17	ELK1	chr4:3079495-3080330	GM12878	blood:	n/a	n/a
18	NFATC1	chr4:3079434-3080207	GM12878	blood:	n/a	n/a
19	NFATC1	chr4:3079376-3080345	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:3079444-3080627	GM12892	blood:	n/a	n/a
21	POLR2A	chr4:3079416-3080553	GM12892	blood:	n/a	n/a
22	MTA3	chr4:3076693-3080356	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:3076052-3080484	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3080079..3082972-chr4:3083884..3086818,3	MCF-7	breast:

Variant related genes	Relation type
HTT-AS	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs110501	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs16843804	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs16843836	0.81[ASN][1000 genomes]
rs17780797	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2024115	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs2071655	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2071704	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs2285086	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285087	0.91[ASN][1000 genomes]
rs28403215	0.85[EUR][1000 genomes]
rs28867436	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs362306	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs362331	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs363063	0.85[EUR][1000 genomes]
rs363064	0.95[CHB][hapmap]
rs363066	0.95[CHB][hapmap]
rs363092	0.80[EUR][1000 genomes]
rs363096	0.95[CHB][hapmap]
rs3905238	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4498089	0.98[ASN][1000 genomes]
rs4690011	0.84[EUR][1000 genomes]
rs4690071	0.91[ASN][1000 genomes]
rs4690072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4690073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs55962025	0.81[ASN][1000 genomes]
rs61348208	0.91[ASN][1000 genomes]
rs6446723	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6844859	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs6855981	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[TSI][hapmap]
rs73191188	0.85[ASN][1000 genomes]
rs762855	0.84[TSI][hapmap]
rs7659144	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7685686	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs7691627	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs82333	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs916171	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856973	OTOP1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3077200-3081000	Weak transcription	Spleen	Spleen
2	chr4:3077400-3093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:3077600-3081400	Weak transcription	Ovary	ovary
4	chr4:3077800-3082400	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:3077800-3084400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:3077800-3089000	Weak transcription	Aorta	Aorta
7	chr4:3077800-3096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:3078000-3081000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:3078000-3081000	Weak transcription	Right Atrium	heart
10	chr4:3078000-3081400	Weak transcription	Right Ventricle	heart
11	chr4:3078000-3082200	Enhancers	Primary B cells from cord blood	blood
12	chr4:3078000-3083400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:3078000-3084200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:3078000-3086200	Weak transcription	Placenta	Placenta
15	chr4:3078000-3086800	Weak transcription	Pancreas	Pancrea
16	chr4:3078000-3088000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:3078000-3088400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:3078000-3088600	Weak transcription	Lung	lung
19	chr4:3078000-3088800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:3078000-3088800	Weak transcription	Thymus	Thymus
21	chr4:3078000-3094600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:3078000-3094600	Weak transcription	Esophagus	oesophagus
23	chr4:3078000-3097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:3078000-3097600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:3078000-3101000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:3078000-3103000	Weak transcription	Colonic Mucosa	Colon
27	chr4:3078200-3089000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:3078200-3089000	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:3078200-3094600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:3078200-3101000	Weak transcription	Brain Substantia Nigra	brain
31	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
32	chr4:3078400-3081000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:3078400-3085400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:3078400-3086800	Weak transcription	NHEK	skin
35	chr4:3078400-3091600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:3078400-3093200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:3078400-3094600	Weak transcription	A549	lung
38	chr4:3078400-3097000	Weak transcription	Brain Anterior Caudate	brain
39	chr4:3078400-3102200	Weak transcription	Hela-S3	cervix
40	chr4:3078400-3107000	Weak transcription	HMEC	breast
41	chr4:3078600-3081000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr4:3078600-3081000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:3078600-3081000	Weak transcription	Fetal Heart	heart
44	chr4:3078600-3081200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr4:3078600-3081600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:3078600-3082600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:3078600-3084200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:3078600-3085400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:3078600-3085800	Enhancers	Primary hematopoietic stem cells	blood
50	chr4:3078600-3086600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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