Variant report

Variant	rs6855981
Chromosome Location	chr4:3148276-3148277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3142213..3145197-chr4:3147789..3149638,3	MCF-7	breast:
2	chr4:3074784..3076813-chr4:3146002..3148347,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251075	Chromatin interaction
ENSG00000197386	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs110501	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs16843804	1.00[CHB][hapmap]
rs16843836	0.83[ASN][1000 genomes]
rs17780797	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1891701	0.98[ASN][1000 genomes]
rs2024115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2071655	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071671	0.89[JPT][hapmap]
rs2071704	0.81[TSI][hapmap]
rs2269477	0.89[ASN][1000 genomes]
rs2269499	0.81[CHD][hapmap]
rs2285086	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap]
rs2285087	0.91[AFR][1000 genomes]
rs2298967	0.88[ASN][1000 genomes]
rs2298971	0.85[ASN][1000 genomes]
rs2798221	0.85[JPT][hapmap]
rs28403215	0.93[ASN][1000 genomes]
rs3095077	0.85[JPT][hapmap]
rs3121419	0.81[JPT][hapmap]
rs362271	0.81[CHD][hapmap]
rs362272	0.81[CHD][hapmap]
rs362273	0.86[CHD][hapmap];0.90[JPT][hapmap]
rs362275	0.81[ASN][1000 genomes]
rs362306	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs362331	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs362336	0.83[ASN][1000 genomes]
rs363063	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs363064	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs363066	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs363088	0.85[ASN][1000 genomes]
rs363092	0.85[ASN][1000 genomes]
rs363096	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs363099	0.87[ASN][1000 genomes]
rs3755883	0.81[ASN][1000 genomes]
rs3856973	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[TSI][hapmap]
rs4690011	0.94[ASN][1000 genomes]
rs4690072	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4690073	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4690075	0.93[ASN][1000 genomes]
rs55962025	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs58666167	0.85[AFR][1000 genomes]
rs59613878	0.97[ASN][1000 genomes]
rs59797128	0.89[AFR][1000 genomes]
rs60197694	0.97[ASN][1000 genomes]
rs61792530	1.00[ASN][1000 genomes]
rs6446722	0.80[ASN][1000 genomes]
rs6446723	0.81[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66684864	0.88[ASN][1000 genomes]
rs6844859	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs73191188	0.87[AFR][1000 genomes]
rs73193303	0.90[ASN][1000 genomes]
rs7659144	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs7685686	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7691627	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs82333	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs916171	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap]

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
rs6855981	OTOP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3088200-3164200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr4:3097200-3162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr4:3097400-3163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:3098000-3162600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:3100000-3159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:3108600-3163000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:3108800-3164600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
9	chr4:3114800-3162800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:3115800-3161600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:3115800-3162800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:3125200-3163000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:3125200-3163200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:3126800-3164400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:3127000-3164400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:3127200-3152600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr4:3127200-3157200	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:3127200-3163400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:3127200-3163400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:3127200-3163400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr4:3127200-3163600	Strong transcription	Fetal Intestine Large	intestine
22	chr4:3127200-3164200	Strong transcription	Fetal Muscle Leg	muscle
23	chr4:3127200-3164400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:3131200-3162600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:3133400-3155000	Weak transcription	Fetal Heart	heart
26	chr4:3134600-3148400	Weak transcription	Psoas Muscle	Psoas
27	chr4:3134600-3148600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:3134800-3162000	Weak transcription	Hela-S3	cervix
29	chr4:3135800-3148600	Weak transcription	Pancreas	Pancrea
30	chr4:3136200-3148400	Weak transcription	NHLF	lung
31	chr4:3136400-3148400	Weak transcription	Ovary	ovary
32	chr4:3136400-3149400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:3136400-3149400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:3136400-3151400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:3136600-3156000	Weak transcription	Stomach Mucosa	stomach
36	chr4:3136800-3148800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:3137400-3148400	Weak transcription	Esophagus	oesophagus
38	chr4:3137800-3163400	Strong transcription	Liver	Liver
39	chr4:3139600-3164800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:3142400-3148400	Weak transcription	Gastric	stomach
41	chr4:3142400-3148400	Weak transcription	Spleen	Spleen
42	chr4:3142600-3148400	Weak transcription	Aorta	Aorta
43	chr4:3142600-3148600	Weak transcription	Lung	lung
44	chr4:3142600-3149000	Weak transcription	K562	blood
45	chr4:3142600-3149600	Weak transcription	Fetal Brain Male	brain
46	chr4:3143000-3148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:3143000-3148400	Weak transcription	NHEK	skin
48	chr4:3143000-3148600	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:3143000-3148800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:3143600-3148600	Weak transcription	Brain Anterior Caudate	brain

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