Variant report

Variant	rs665943
Chromosome Location	chr3:50619906-50619907
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
2	chr3:50614914..50616953-chr3:50617610..50620432,2	MCF-7	breast:
3	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
4	chr3:50378822..50381164-chr3:50619483..50621756,2	K562	blood:
5	chr3:50607065..50611118-chr3:50617412..50623416,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114737	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000004838	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1038415	1.00[EUR][1000 genomes]
rs107457	1.00[EUR][1000 genomes]
rs1552255	1.00[EUR][1000 genomes]
rs1552256	1.00[EUR][1000 genomes]
rs17051012	1.00[EUR][1000 genomes]
rs17051016	1.00[EUR][1000 genomes]
rs17051017	1.00[EUR][1000 genomes]
rs17051404	1.00[EUR][1000 genomes]
rs1843073	1.00[EUR][1000 genomes]
rs2232251	1.00[EUR][1000 genomes]
rs2262848	1.00[EUR][1000 genomes]
rs2355337	1.00[EUR][1000 genomes]
rs2355701	1.00[EUR][1000 genomes]
rs2459450	1.00[EUR][1000 genomes]
rs2609015	1.00[EUR][1000 genomes]
rs2609027	1.00[EUR][1000 genomes]
rs2609030	1.00[EUR][1000 genomes]
rs2675781	1.00[EUR][1000 genomes]
rs2675785	1.00[EUR][1000 genomes]
rs2675823	1.00[EUR][1000 genomes]
rs2675824	1.00[EUR][1000 genomes]
rs2675826	1.00[EUR][1000 genomes]
rs2675833	1.00[EUR][1000 genomes]
rs407164	1.00[EUR][1000 genomes]
rs421689	1.00[EUR][1000 genomes]
rs4234694	1.00[EUR][1000 genomes]
rs4234695	1.00[EUR][1000 genomes]
rs4267639	1.00[EUR][1000 genomes]
rs4340700	1.00[EUR][1000 genomes]
rs4688704	1.00[EUR][1000 genomes]
rs55852678	1.00[EUR][1000 genomes]
rs56112107	1.00[EUR][1000 genomes]
rs56198179	1.00[EUR][1000 genomes]
rs56341000	1.00[EUR][1000 genomes]
rs56413944	1.00[EUR][1000 genomes]
rs57756789	1.00[EUR][1000 genomes]
rs57987466	1.00[EUR][1000 genomes]
rs58854038	1.00[EUR][1000 genomes]
rs58911362	1.00[EUR][1000 genomes]
rs59065723	1.00[EUR][1000 genomes]
rs59337835	1.00[EUR][1000 genomes]
rs59340349	1.00[EUR][1000 genomes]
rs60132317	1.00[EUR][1000 genomes]
rs60455882	1.00[EUR][1000 genomes]
rs609678	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61032466	1.00[EUR][1000 genomes]
rs61455710	1.00[EUR][1000 genomes]
rs621975	1.00[EUR][1000 genomes]
rs628865	1.00[EUR][1000 genomes]
rs6446223	1.00[EUR][1000 genomes]
rs650473	1.00[EUR][1000 genomes]
rs667894	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6768539	1.00[EUR][1000 genomes]
rs6789552	1.00[EUR][1000 genomes]
rs73833231	1.00[EUR][1000 genomes]
rs73833232	1.00[EUR][1000 genomes]
rs73833239	1.00[EUR][1000 genomes]
rs73833247	1.00[EUR][1000 genomes]
rs73833935	1.00[EUR][1000 genomes]
rs73835518	1.00[EUR][1000 genomes]
rs73835533	1.00[EUR][1000 genomes]
rs73835535	1.00[EUR][1000 genomes]
rs73835537	1.00[EUR][1000 genomes]
rs73835538	1.00[EUR][1000 genomes]
rs936714	1.00[EUR][1000 genomes]
rs9840476	1.00[EUR][1000 genomes]
rs9851304	1.00[EUR][1000 genomes]
rs9857033	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
2	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
5	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
8	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:50608200-50628400	Weak transcription	A549	lung
11	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
12	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
13	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
14	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
15	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:50610200-50620400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr3:50610200-50623600	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:50610200-50624400	Strong transcription	Fetal Stomach	stomach
20	chr3:50610200-50628000	Weak transcription	Stomach Mucosa	stomach
21	chr3:50610400-50622400	Weak transcription	GM12878-XiMat	blood
22	chr3:50610400-50623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:50610400-50623200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:50610400-50628400	Weak transcription	HSMM	muscle
25	chr3:50610600-50627600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:50611000-50620600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:50611200-50621600	Strong transcription	Thymus	Thymus
28	chr3:50611400-50621600	Strong transcription	Fetal Intestine Small	intestine
29	chr3:50612200-50621400	Strong transcription	Fetal Intestine Large	intestine
30	chr3:50612400-50620600	Strong transcription	Spleen	Spleen
31	chr3:50613000-50620000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:50613000-50620600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:50613000-50622400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:50613400-50620400	Strong transcription	Gastric	stomach
35	chr3:50613400-50621200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:50613400-50628000	Weak transcription	HMEC	breast
37	chr3:50613600-50621400	Strong transcription	Esophagus	oesophagus
38	chr3:50613800-50621200	Strong transcription	Brain Substantia Nigra	brain
39	chr3:50614000-50620200	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:50614200-50620000	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr3:50614200-50620200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:50614200-50620200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:50614200-50620400	Strong transcription	Brain Anterior Caudate	brain
44	chr3:50614400-50620400	Strong transcription	Colonic Mucosa	Colon
45	chr3:50614400-50620600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:50614400-50621800	Strong transcription	Dnd41	blood
47	chr3:50614600-50621800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:50614800-50620400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:50614800-50620800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:50615600-50620200	Weak transcription	Aorta	Aorta

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