Variant report

Variant	rs2470856
Chromosome Location	chr3:98596662-98596663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98595066..98597311-chr3:98599043..98600864,2	K562	blood:
2	chr3:98595385..98598220-chr3:98601282..98604965,3	K562	blood:
3	chr3:98596084..98598965-chr3:98619062..98620700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.95[AFR][1000 genomes]
rs2173598	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.84[AFR][1000 genomes]
rs2470828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.95[AFR][1000 genomes]
rs278375	0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929491	0.84[AFR][1000 genomes]
rs4273318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5013928	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440189	0.84[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.92[AFR][1000 genomes]
rs7373983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73858658	0.81[AFR][1000 genomes]
rs7626395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.85[YRI][hapmap]
rs828619	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs974982	0.81[AFR][1000 genomes]
rs9883226	1.00[YRI][hapmap]
rs996199	1.00[YRI][hapmap];0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98576000-98598600	Weak transcription	Fetal Kidney	kidney
6	chr3:98577200-98598800	Weak transcription	Left Ventricle	heart
7	chr3:98578000-98601000	Weak transcription	Lung	lung
8	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:98584600-98604200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:98586600-98598600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:98587200-98604600	Weak transcription	Ovary	ovary
13	chr3:98587800-98601800	Strong transcription	HSMM	muscle
14	chr3:98589000-98598600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:98589200-98602200	Weak transcription	NHLF	lung
16	chr3:98589400-98598800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
18	chr3:98589600-98597000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:98589600-98599800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:98589800-98604000	Weak transcription	Fetal Stomach	stomach
21	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
22	chr3:98590800-98597000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:98590800-98598600	Weak transcription	HSMMtube	muscle
24	chr3:98590800-98604600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:98591000-98598000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:98591000-98598600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:98591200-98597000	Weak transcription	Fetal Lung	lung
28	chr3:98591200-98599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:98591400-98597200	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:98591400-98598600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:98591400-98598600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:98591400-98598600	Weak transcription	Liver	Liver
33	chr3:98591400-98598800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:98591400-98602200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:98591400-98604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:98591600-98598600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:98591600-98600000	Weak transcription	Dnd41	blood
38	chr3:98591600-98604600	Weak transcription	Aorta	Aorta
39	chr3:98592000-98597600	Strong transcription	NHDF-Ad	bronchial
40	chr3:98592000-98598600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:98592600-98604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:98593000-98598800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:98593200-98599200	Weak transcription	Fetal Brain Female	brain
44	chr3:98593400-98597600	Enhancers	Fetal Heart	heart
45	chr3:98593600-98597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:98593600-98599000	Genic enhancers	NH-A	brain
47	chr3:98593800-98597800	Genic enhancers	Osteobl	bone
48	chr3:98593800-98604600	Weak transcription	Psoas Muscle	Psoas
49	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
50	chr3:98594000-98598600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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