Variant report

Variant	rs1369279
Chromosome Location	chr3:191058537-191058538
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	chr3:191047482..191049844-chr3:191056418..191059474,3	MCF-7	breast:
2	chr3:191045847..191048975-chr3:191057360..191059189,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188958	Chromatin interaction
ENSG00000152492	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10513865	0.87[CEU][hapmap];0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs1369278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474188	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16822368	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16822380	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16822489	1.00[CEU][hapmap]
rs16848976	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16866501	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866503	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866506	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2117548	0.87[CEU][hapmap];0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2293379	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs4247189	1.00[ASN][1000 genomes]
rs4247190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4677724	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677731	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57369465	1.00[ASN][1000 genomes]
rs57831251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58077600	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58596458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58631024	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58648691	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60089463	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60204557	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9812544	0.80[ASN][1000 genomes]

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	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191049000-191058600	Weak transcription	Left Ventricle	heart
2	chr3:191049200-191060600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:191049800-191061600	Weak transcription	HSMMtube	muscle
4	chr3:191050200-191060200	Weak transcription	Psoas Muscle	Psoas
5	chr3:191050200-191074800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:191050600-191060400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:191051200-191060200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:191051400-191058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:191051400-191059400	Weak transcription	Right Atrium	heart
10	chr3:191051400-191060000	Weak transcription	Brain Germinal Matrix	brain
11	chr3:191051400-191060200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:191051400-191060200	Weak transcription	Right Ventricle	heart
13	chr3:191052200-191062400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:191053200-191059200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:191055000-191059200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:191055400-191061800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:191055600-191062000	Enhancers	HepG2	liver
18	chr3:191056000-191061000	Enhancers	Liver	Liver
19	chr3:191056200-191062200	Enhancers	Fetal Brain Male	brain
20	chr3:191056200-191063400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:191056400-191059200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:191056400-191060000	Weak transcription	HSMM	muscle
23	chr3:191056600-191059200	Weak transcription	A549	lung
24	chr3:191056800-191062000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:191057000-191059800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:191057400-191059000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:191057400-191059000	Weak transcription	GM12878-XiMat	blood
28	chr3:191057400-191059400	Weak transcription	NHLF	lung
29	chr3:191057400-191062000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:191057600-191059400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:191057600-191060000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:191057600-191060400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:191057600-191060400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:191057600-191060400	Weak transcription	Primary B cells from cord blood	blood
35	chr3:191057600-191060800	Weak transcription	NH-A	brain
36	chr3:191057800-191058600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:191057800-191059200	Weak transcription	Small Intestine	intestine
38	chr3:191057800-191059200	Weak transcription	Osteobl	bone
39	chr3:191057800-191059800	Weak transcription	Fetal Lung	lung
40	chr3:191057800-191059800	Weak transcription	Hela-S3	cervix
41	chr3:191057800-191060200	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:191057800-191060400	Weak transcription	NHDF-Ad	bronchial
43	chr3:191057800-191060800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:191057800-191061600	Weak transcription	K562	blood
45	chr3:191057800-191061800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:191057800-191062600	Weak transcription	Aorta	Aorta
47	chr3:191058000-191058600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:191058000-191059200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:191058000-191059200	Weak transcription	HUVEC	blood vessel
50	chr3:191058000-191060600	Weak transcription	NHEK	skin

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