Variant report

Variant	rs4858812
Chromosome Location	chr3:47480526-47480527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47479631..47481186-chr3:47484843..47486561,2	MCF-7	breast:
2	chr3:47473262..47475459-chr3:47480046..47481718,2	K562	blood:
3	chr3:47476704..47482785-chr3:47483976..47487326,5	K562	blood:
4	chr3:47478177..47481033-chr3:47516473..47518290,2	MCF-7	breast:
5	chr3:47471198..47476124-chr3:47477779..47481546,5	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1024036	1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1038393	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	1.00[YRI][hapmap]
rs12631697	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13077134	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs1531874	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	0.91[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6442068	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778673	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6788978	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.87[AMR][1000 genomes]
rs7639121	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.90[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900693	0.90[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs900694	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs903538	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs924009	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859947	1.00[MEX][hapmap]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:47463400-47484600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
5	chr3:47464000-47484200	Weak transcription	Right Atrium	heart
6	chr3:47465400-47484600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:47465600-47484200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr3:47469200-47484400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:47470000-47481200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:47471800-47485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:47472000-47482200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:47472000-47484600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:47472400-47484600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:47472400-47485200	Weak transcription	Fetal Brain Male	brain
15	chr3:47472800-47484400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:47473200-47483600	Weak transcription	Fetal Heart	heart
17	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
18	chr3:47473400-47481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:47474000-47481600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr3:47474000-47483600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:47475000-47484600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:47475800-47481000	Weak transcription	Gastric	stomach
24	chr3:47475800-47481000	Weak transcription	Hela-S3	cervix
25	chr3:47475800-47482800	Weak transcription	NHDF-Ad	bronchial
26	chr3:47476000-47483800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:47476000-47484200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:47476000-47484200	Weak transcription	Colonic Mucosa	Colon
29	chr3:47476000-47485800	Weak transcription	Fetal Kidney	kidney
30	chr3:47476200-47481000	Weak transcription	Osteobl	bone
31	chr3:47476600-47480800	Weak transcription	Ovary	ovary
32	chr3:47476600-47480800	Weak transcription	Thymus	Thymus
33	chr3:47476600-47481000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:47476600-47481000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:47476600-47481000	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:47476600-47481000	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:47476600-47481000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:47476600-47481000	Weak transcription	Esophagus	oesophagus
39	chr3:47476600-47481000	Weak transcription	Pancreas	Pancrea
40	chr3:47476600-47481000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:47476600-47481000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:47476600-47481000	Weak transcription	Spleen	Spleen
43	chr3:47476600-47481000	Weak transcription	NHLF	lung
44	chr3:47476600-47481200	Weak transcription	NHEK	skin
45	chr3:47476600-47483000	Weak transcription	GM12878-XiMat	blood
46	chr3:47476600-47483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:47476600-47483800	Weak transcription	Psoas Muscle	Psoas
48	chr3:47476600-47484000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:47476600-47484200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:47476600-47484200	Weak transcription	Small Intestine	intestine

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