Variant report

Variant	rs41265402
Chromosome Location	chr3:178947684-178947685
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178945435..178949746-chr3:178950084..178953844,5	K562	blood:
2	chr3:178945786..178948159-chr3:178949089..178951584,2	K562	blood:
3	chr3:178946686..178948186-chr8:146053818..146055345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147789	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs3729692	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41273619	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55710741	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56034093	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57210103	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57620676	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60976095	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73882973	0.84[AMR][1000 genomes];0.93[EUR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv878038	chr3:178924867-178962897	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878039	chr3:178933363-178968568	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv965236	chr3:178938931-178955061	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178899200-178951800	Weak transcription	K562	blood
2	chr3:178906400-178962400	Weak transcription	HepG2	liver
3	chr3:178911200-178953400	Weak transcription	Gastric	stomach
4	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
5	chr3:178912600-178947800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:178913000-178948200	Weak transcription	Psoas Muscle	Psoas
7	chr3:178913800-178954000	Weak transcription	Fetal Heart	heart
8	chr3:178913800-178969000	Weak transcription	Small Intestine	intestine
9	chr3:178914800-178948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:178914800-178972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:178915800-178965200	Weak transcription	Hela-S3	cervix
12	chr3:178917400-178948400	Weak transcription	Esophagus	oesophagus
13	chr3:178917600-178953800	Weak transcription	Colonic Mucosa	Colon
14	chr3:178920200-178947800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:178920200-178948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:178920200-178952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:178920200-178968400	Weak transcription	Spleen	Spleen
18	chr3:178921200-178948800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:178924200-178948200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:178925800-178951600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:178925800-178968200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:178925800-178968600	Weak transcription	Pancreas	Pancrea
23	chr3:178928600-178962400	Weak transcription	Brain Substantia Nigra	brain
24	chr3:178928800-178948600	Weak transcription	Fetal Kidney	kidney
25	chr3:178928800-178953200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:178929200-178954000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:178929400-178948600	Weak transcription	Brain Anterior Caudate	brain
28	chr3:178929800-178962800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:178930600-178954200	Weak transcription	Fetal Intestine Small	intestine
30	chr3:178931400-178948000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:178931800-178948200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:178931800-178951400	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:178932200-178974000	Weak transcription	Lung	lung
34	chr3:178935600-178949200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:178936000-178952400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr3:178936200-178949400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:178938200-178949200	Strong transcription	Dnd41	blood
38	chr3:178938200-178952400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:178938800-178949200	Strong transcription	Liver	Liver
40	chr3:178938800-178950400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:178938800-178954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:178939200-178949800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:178940000-178948200	Weak transcription	Fetal Stomach	stomach
44	chr3:178940600-178948200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:178941200-178947800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:178941800-178972600	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:178942800-178950200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr3:178942800-178965400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:178943200-178947800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:178943400-178949200	Strong transcription	Primary B cells from cord blood	blood

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