Variant report

Variant	rs110501
Chromosome Location	chr4:3225478-3225479
allele	A/G
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	chr4:3225396-3225650	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:3225305-3225988	K562	blood:	n/a	n/a
3	POLR2A	chr4:3225400-3225635	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:3225360-3225521	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs16843804	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs17780797	0.83[EUR][1000 genomes]
rs2024115	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs2071655	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2071662	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071671	0.94[JPT][hapmap]
rs2071704	1.00[ASW][hapmap];0.84[CEU][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs2157090	0.81[JPT][hapmap]
rs2237006	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2237007	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2269478	0.87[EUR][1000 genomes]
rs2269499	0.80[JPT][hapmap]
rs2276882	0.84[AMR][1000 genomes]
rs2285086	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2298967	0.80[ASN][1000 genomes]
rs2298971	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2530598	0.82[EUR][1000 genomes]
rs2530601	0.81[JPT][hapmap]
rs2798221	0.90[JPT][hapmap]
rs28403215	0.86[EUR][1000 genomes]
rs3095077	0.90[JPT][hapmap]
rs3121419	0.85[JPT][hapmap]
rs362271	0.80[JPT][hapmap]
rs362272	0.80[JPT][hapmap]
rs362273	0.95[JPT][hapmap]
rs362275	0.88[ASN][1000 genomes]
rs362296	0.84[JPT][hapmap]
rs362306	0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs362309	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs362314	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs362319	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs362331	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs362336	0.84[ASN][1000 genomes]
rs363063	0.82[EUR][1000 genomes]
rs363064	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs363066	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs363088	0.83[ASN][1000 genomes]
rs363091	0.83[LWK][hapmap];0.84[MKK][hapmap]
rs363092	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs363096	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3755883	0.87[ASN][1000 genomes]
rs3856973	0.96[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs4690011	0.87[EUR][1000 genomes]
rs4690072	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs4690073	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6446723	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs6446727	0.81[JPT][hapmap]
rs6446731	0.81[JPT][hapmap]
rs6834455	0.83[LWK][hapmap]
rs6844859	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855981	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs7659144	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs7661630	0.81[JPT][hapmap]
rs7665816	0.81[LWK][hapmap]
rs7685686	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7691627	0.96[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs82332	0.89[ASN][1000 genomes]
rs82333	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs82334	0.89[ASN][1000 genomes]
rs916171	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996868	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
10	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs110501	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	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
7	chr4:3201400-3238400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:3204800-3246000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:3205800-3228000	Strong transcription	Left Ventricle	heart
10	chr4:3206000-3234800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:3206000-3244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:3206000-3246400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:3206400-3229600	Strong transcription	Fetal Stomach	stomach
14	chr4:3207200-3229000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:3207600-3238600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:3207600-3243600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr4:3207600-3244000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:3207600-3244600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:3207600-3245400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:3207600-3246400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:3207800-3226400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:3207800-3226600	Strong transcription	Primary B cells from cord blood	blood
23	chr4:3207800-3228200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr4:3207800-3228400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr4:3207800-3229000	Strong transcription	Aorta	Aorta
26	chr4:3207800-3229800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:3207800-3243200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:3207800-3243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:3207800-3244400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:3207800-3245400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:3208000-3227000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr4:3208000-3235800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:3208000-3243600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:3208200-3227200	Strong transcription	NH-A	brain
35	chr4:3208200-3228400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:3208200-3237400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:3208200-3239200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:3208200-3246400	Strong transcription	Fetal Thymus	thymus
39	chr4:3208400-3226800	Strong transcription	Brain Hippocampus Middle	brain
40	chr4:3208400-3228000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr4:3208400-3228000	Strong transcription	Colonic Mucosa	Colon
42	chr4:3208400-3244800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:3209800-3227200	Strong transcription	Osteobl	bone
44	chr4:3209800-3229400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:3210000-3228000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:3210000-3230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:3210000-3244200	Strong transcription	Fetal Intestine Large	intestine
48	chr4:3210000-3245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:3210000-3246600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:3210200-3230800	Strong transcription	Spleen	Spleen

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