Variant report

Variant	rs1440157
Chromosome Location	chr3:98612810-98612811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98602528..98604913-chr3:98611525..98613667,2	K562	blood:
2	chr3:98612045..98613776-chr3:98618564..98620858,2	MCF-7	breast:
3	chr3:98610185..98614055-chr3:98618710..98621878,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1531736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	0.97[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.98[AFR][1000 genomes]
rs2173598	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.88[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs2470828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470856	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.98[AFR][1000 genomes]
rs278375	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929491	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs4273318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5013928	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440189	0.81[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.95[AFR][1000 genomes]
rs7373983	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73858658	0.81[AFR][1000 genomes]
rs7626395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.92[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.92[YRI][hapmap]
rs828619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	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];0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
3	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
5	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
8	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
9	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:98604000-98613000	Enhancers	NHLF	lung
11	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
13	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
14	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:98608800-98614400	Enhancers	K562	blood
16	chr3:98609000-98613200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:98609000-98615800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:98609200-98613400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:98609400-98613400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:98609400-98613800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:98609600-98613400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:98609800-98613800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:98609800-98614200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:98610400-98615000	Transcr. at gene 5' and 3'	Osteobl	bone
25	chr3:98610400-98615800	Transcr. at gene 5' and 3'	NH-A	brain
26	chr3:98610400-98616600	Transcr. at gene 5' and 3'	A549	lung
27	chr3:98610600-98613400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr3:98610800-98614200	Enhancers	Right Ventricle	heart
29	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
31	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:98611000-98613200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:98611000-98613200	Enhancers	HepG2	liver
34	chr3:98611200-98613400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:98611200-98617000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:98611600-98613000	Enhancers	Adipose Nuclei	Adipose
39	chr3:98611600-98616600	Weak transcription	Fetal Lung	lung
40	chr3:98611800-98613200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:98611800-98613400	Genic enhancers	HUVEC	blood vessel
42	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:98612000-98613400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:98612000-98613600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:98612000-98614800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
48	chr3:98612200-98613000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:98612400-98613200	Enhancers	Aorta	Aorta
50	chr3:98612400-98613200	Enhancers	Brain Hippocampus Middle	brain

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