Variant report

Variant	rs73201630
Chromosome Location	chr3:191053583-191053584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191048783..191051594-chr3:191052862..191055527,3	MCF-7	breast:
2	chr3:191046891..191049504-chr3:191051045..191053812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188958	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11542549	0.89[ASN][1000 genomes]
rs1435062	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1473869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1520202	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520203	0.90[ASN][1000 genomes]
rs1609926	0.93[EUR][1000 genomes]
rs16822378	0.93[EUR][1000 genomes]
rs16822382	0.93[EUR][1000 genomes]
rs16866487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16866504	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16866505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17753967	0.84[ASN][1000 genomes]
rs17810246	0.84[ASN][1000 genomes]
rs17810282	0.84[ASN][1000 genomes]
rs17838893	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2056333	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364379	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28715898	0.84[ASN][1000 genomes]
rs3796219	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677631	0.84[ASN][1000 genomes]
rs4677632	0.84[ASN][1000 genomes]
rs4677725	0.84[ASN][1000 genomes]
rs4677726	0.84[ASN][1000 genomes]
rs4677727	0.84[ASN][1000 genomes]
rs56174842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57211729	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58141749	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58645265	0.89[ASN][1000 genomes]
rs59709586	0.91[EUR][1000 genomes]
rs61250936	0.88[EUR][1000 genomes]
rs6444541	0.84[ASN][1000 genomes]
rs73185209	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73185210	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73185213	0.89[ASN][1000 genomes]
rs73185226	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73185228	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73185240	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73185255	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73185263	0.93[EUR][1000 genomes]
rs73185284	0.91[EUR][1000 genomes]
rs73185287	0.91[EUR][1000 genomes]
rs73185288	0.91[EUR][1000 genomes]
rs73201627	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637196	0.84[ASN][1000 genomes]
rs7642387	0.84[ASN][1000 genomes]
rs7648886	0.84[ASN][1000 genomes]
rs9290986	0.84[ASN][1000 genomes]
rs9823680	0.84[ASN][1000 genomes]
rs9824437	0.84[ASN][1000 genomes]
rs9839751	0.80[ASN][1000 genomes]
rs9843934	0.84[ASN][1000 genomes]
rs9853569	0.84[ASN][1000 genomes]
rs9863255	0.86[ASN][1000 genomes]
rs9876944	0.83[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:66 , 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	chr3:191049400-191057600	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:191049800-191061600	Weak transcription	HSMMtube	muscle
5	chr3:191050000-191055600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:191050000-191056400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:191050000-191057200	Weak transcription	Fetal Lung	lung
8	chr3:191050200-191054400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:191050200-191054800	Enhancers	HepG2	liver
10	chr3:191050200-191055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:191050200-191060200	Weak transcription	Psoas Muscle	Psoas
12	chr3:191050200-191074800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:191050400-191054600	Weak transcription	Osteobl	bone
14	chr3:191050600-191060400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:191050800-191057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:191050800-191057800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:191051000-191055400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:191051000-191055400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:191051000-191055800	Weak transcription	HMEC	breast
20	chr3:191051000-191056000	Weak transcription	HSMM	muscle
21	chr3:191051000-191056000	Enhancers	HUVEC	blood vessel
22	chr3:191051200-191060200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:191051400-191053600	Weak transcription	Small Intestine	intestine
24	chr3:191051400-191054600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:191051400-191054600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:191051400-191055400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:191051400-191055800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:191051400-191056000	Weak transcription	Fetal Heart	heart
29	chr3:191051400-191056000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:191051400-191057200	Weak transcription	Aorta	Aorta
31	chr3:191051400-191057400	Weak transcription	Ovary	ovary
32	chr3:191051400-191058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:191051400-191059400	Weak transcription	Right Atrium	heart
34	chr3:191051400-191060000	Weak transcription	Brain Germinal Matrix	brain
35	chr3:191051400-191060200	Weak transcription	Brain Anterior Caudate	brain
36	chr3:191051400-191060200	Weak transcription	Right Ventricle	heart
37	chr3:191051600-191054400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:191051600-191057000	Weak transcription	Fetal Brain Female	brain
39	chr3:191052000-191054000	Enhancers	NH-A	brain
40	chr3:191052000-191054200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:191052200-191053600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:191052200-191062400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:191052400-191054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:191052400-191054000	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr3:191052400-191056200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:191052400-191056200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:191052400-191057800	Enhancers	Hela-S3	cervix
48	chr3:191052600-191054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:191052600-191055200	Weak transcription	NHEK	skin
50	chr3:191052600-191057200	Weak transcription	Brain Hippocampus Middle	brain

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