Variant report

Variant	rs3849700
Chromosome Location	chr5:43061027-43061028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43060782-43061265	K562	blood:	n/a	n/a
2	POLR2A	chr5:43060835-43061035	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:43060977-43061099	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF263	chr5:43060806-43061816	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43038662..43048059-chr5:43059399..43070773,40	MCF-7	breast:
2	chr5:43036901..43050217-chr5:43060442..43069391,53	MCF-7	breast:
3	chr5:43060081..43061989-chr5:43067266..43069367,2	MCF-7	breast:
4	chr5:43056723..43061156-chr5:43062067..43067784,7	K562	blood:

Variant related genes	Relation type
ENSG00000272144	TF binding region
ZNF131	TF binding region
ENSG00000172262	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1001718	1.00[AMR][1000 genomes]
rs10070393	1.00[AMR][1000 genomes]
rs28659803	1.00[AMR][1000 genomes]
rs55730625	1.00[AMR][1000 genomes]
rs60384612	1.00[AMR][1000 genomes]
rs61328340	1.00[AMR][1000 genomes]
rs6859504	1.00[AMR][1000 genomes]
rs6860747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6864556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6869639	1.00[AMR][1000 genomes]
rs6875245	1.00[AMR][1000 genomes]
rs6877778	1.00[AMR][1000 genomes]
rs6879509	1.00[AMR][1000 genomes]
rs6881357	1.00[AMR][1000 genomes]
rs6886169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6887110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6891509	1.00[AMR][1000 genomes]
rs6891660	1.00[AMR][1000 genomes]
rs6895975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6897663	1.00[AMR][1000 genomes]
rs73088862	1.00[AMR][1000 genomes]
rs73088863	1.00[AMR][1000 genomes]
rs73088878	1.00[AMR][1000 genomes]
rs73754524	1.00[AMR][1000 genomes]
rs73754532	1.00[AMR][1000 genomes]
rs747118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs747119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7703982	1.00[AMR][1000 genomes]
rs7710205	1.00[AMR][1000 genomes]
rs7717370	1.00[AMR][1000 genomes]
rs7718462	1.00[AMR][1000 genomes]
rs7737740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active 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 miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
9	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43043600-43061600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:43043600-43063800	Weak transcription	Aorta	Aorta
3	chr5:43043600-43064000	Weak transcription	NHEK	skin
4	chr5:43043800-43061200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:43043800-43064000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:43044800-43064000	Weak transcription	Right Ventricle	heart
7	chr5:43044800-43064200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:43044800-43064400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:43045000-43061400	Weak transcription	NHLF	lung
10	chr5:43045000-43063800	Weak transcription	Adipose Nuclei	Adipose
11	chr5:43045000-43064200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:43045000-43064400	Weak transcription	Esophagus	oesophagus
13	chr5:43045400-43061400	Weak transcription	Hela-S3	cervix
14	chr5:43045400-43064200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:43045400-43066000	Weak transcription	Spleen	Spleen
16	chr5:43045600-43063600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:43046600-43063800	Weak transcription	Left Ventricle	heart
18	chr5:43048200-43064200	Weak transcription	Psoas Muscle	Psoas
19	chr5:43049200-43064000	Weak transcription	Fetal Stomach	stomach
20	chr5:43049400-43061200	Weak transcription	HSMM	muscle
21	chr5:43049400-43061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:43049800-43064400	Weak transcription	Fetal Lung	lung
23	chr5:43050000-43061400	Weak transcription	NH-A	brain
24	chr5:43050600-43061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:43050800-43064000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:43051400-43064400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:43051600-43064600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:43052600-43063800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:43053400-43064000	Weak transcription	Primary T cells from cord blood	blood
30	chr5:43053600-43064000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:43053600-43064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:43053800-43063600	Weak transcription	Dnd41	blood
33	chr5:43053800-43063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:43053800-43063800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:43053800-43063800	Weak transcription	Placenta	Placenta
36	chr5:43053800-43063800	Weak transcription	Fetal Thymus	thymus
37	chr5:43053800-43063800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:43053800-43064000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:43054000-43063800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:43054400-43063800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:43054400-43063800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:43058600-43061200	Weak transcription	Osteobl	bone
43	chr5:43058800-43061200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:43059000-43061400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:43059000-43063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:43059000-43063800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:43059000-43063800	Weak transcription	Thymus	Thymus
48	chr5:43059000-43063800	Weak transcription	HSMMtube	muscle
49	chr5:43059200-43063600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:43059200-43063800	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links