Variant report

Variant	rs7658340
Chromosome Location	chr4:57304583-57304584
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57302424..57305158-chr4:57338707..57340415,2	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
3	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
4	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
5	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1140982	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1142851	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11934479	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11934636	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11940993	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12643989	0.92[ASN][1000 genomes]
rs12643996	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12644498	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12649799	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12650288	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1579019	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17086773	0.94[ASN][1000 genomes]
rs17086801	0.94[ASN][1000 genomes]
rs17086804	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17086830	0.92[ASN][1000 genomes]
rs17086838	0.92[ASN][1000 genomes]
rs17086868	0.92[ASN][1000 genomes]
rs17086898	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17086909	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17086919	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17086922	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34398021	0.92[ASN][1000 genomes]
rs34419325	0.92[ASN][1000 genomes]
rs3796549	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3796550	0.94[ASN][1000 genomes]
rs4076103	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56362514	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57245446	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59828502	0.92[ASN][1000 genomes]
rs6830145	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6831869	0.86[AMR][1000 genomes]
rs7688482	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7658340	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
2	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
3	chr4:57299200-57304800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:57299200-57305000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:57299400-57304800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:57299400-57305000	Active TSS	K562	blood
10	chr4:57299800-57304800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:57299800-57305600	Active TSS	HepG2	liver
12	chr4:57301600-57304800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:57301600-57305200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
16	chr4:57303800-57308400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:57303800-57326000	Weak transcription	Gastric	stomach
18	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
19	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
20	chr4:57304000-57304800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr4:57304000-57305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:57304000-57306800	Enhancers	Liver	Liver
23	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
24	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
26	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
27	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
28	chr4:57304200-57305000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:57304200-57305200	Weak transcription	Colonic Mucosa	Colon
30	chr4:57304200-57305600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:57304200-57305800	Weak transcription	Brain Angular Gyrus	brain
32	chr4:57304200-57305800	Weak transcription	Fetal Thymus	thymus
33	chr4:57304200-57306400	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:57304200-57307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:57304200-57307800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:57304200-57308000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:57304200-57308000	Weak transcription	Placenta	Placenta
38	chr4:57304200-57308200	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
42	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:57304400-57304600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:57304400-57304600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr4:57304400-57304600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:57304400-57304600	Enhancers	NH-A	brain
49	chr4:57304400-57304600	Enhancers	NHEK	skin
50	chr4:57304400-57304800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links