Variant report

Variant	rs58200674
Chromosome Location	chr4:129512391-129512392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129507964..129509503-chr4:129511256..129514163,2	MCF-7	breast:
2	chr4:129496152..129497734-chr4:129511313..129514050,2	MCF-7	breast:
3	chr4:129506598..129509116-chr4:129512243..129515091,2	K562	blood:
4	chr4:129509584..129513503-chr4:129730638..129733313,3	K562	blood:
5	chr4:129512305..129514760-chr4:129521336..129523265,2	K562	blood:

Variant related genes	Relation type
ENSG00000248802	Chromatin interaction
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17013484	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17013486	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57357435	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58160513	0.93[EUR][1000 genomes]
rs59261281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60593095	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60917665	0.90[EUR][1000 genomes]
rs60972557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932244	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72932252	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72932254	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932256	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932261	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	79 gene(s)	inside rSNPs	diseases
2	nsv1017672	chr4:129450450-129603977	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129505800-129520400	Weak transcription	Gastric	stomach
2	chr4:129506000-129512400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:129507000-129512400	Weak transcription	Placenta	Placenta
4	chr4:129509200-129512400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr4:129510000-129514200	Enhancers	Fetal Heart	heart
6	chr4:129510200-129513200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr4:129510600-129513000	Enhancers	Fetal Muscle Leg	muscle
8	chr4:129510800-129512400	Enhancers	Stomach Smooth Muscle	stomach
9	chr4:129510800-129512600	Enhancers	Brain Germinal Matrix	brain
10	chr4:129510800-129513000	Enhancers	A549	lung
11	chr4:129511000-129512600	Enhancers	HSMMtube	muscle
12	chr4:129511000-129512800	Enhancers	Left Ventricle	heart
13	chr4:129511400-129512400	Weak transcription	Pancreas	Pancrea
14	chr4:129511400-129512600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:129511600-129512600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr4:129511600-129512600	Weak transcription	Psoas Muscle	Psoas
17	chr4:129511600-129512800	Weak transcription	Fetal Kidney	kidney
18	chr4:129511600-129512800	Weak transcription	HepG2	liver
19	chr4:129511800-129512600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:129511800-129519800	Weak transcription	Right Ventricle	heart
21	chr4:129512000-129513000	Enhancers	Fetal Muscle Trunk	muscle
22	chr4:129512200-129512600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr4:129512200-129512600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:129512200-129517200	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links