Variant report

Variant	rs58351439
Chromosome Location	chr4:48273827-48273828
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	SETDB1	chr4:48273231-48273981	U2OS	brain:	n/a	n/a
2	KAP1	chr4:48272095-48273922	HEK293	kidney:	n/a	n/a
3	MAFK	chr4:48271899-48274278	GM12878	blood:	n/a	chr4:48273198-48273213
4	CBX3	chr4:48273536-48274046	K562	blood:	n/a	n/a
5	POLR2A	chr4:48270681-48274063	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48272391..48273974-chr4:48279554..48281442,2	MCF-7	breast:

Variant related genes	Relation type
TEC	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10938525	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11724904	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726643	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727166	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732863	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735909	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11932711	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933797	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11934755	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11945482	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947315	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472970	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17655431	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17655449	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008107	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353296	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2457409	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2664025	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4340766	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55702720	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57233179	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58275144	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58620171	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59336353	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59720516	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61010385	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447628	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835303	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835363	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6835615	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845740	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6857308	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73817607	0.91[EUR][1000 genomes]
rs7655057	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7682629	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906901	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs925288	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2763359	chr4:48189710-48290233	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv461357	chr4:48248258-48274152	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv594119	chr4:48248258-48274152	Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv470032	chr4:48251915-48312389	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv461358	chr4:48251916-48274152	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv594120	chr4:48251916-48274152	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48272400-48274600	Weak transcription	Pancreas	Pancrea
2	chr4:48272600-48274000	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:48272600-48276600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:48272800-48275200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:48272800-48277200	Weak transcription	Fetal Lung	lung
6	chr4:48273000-48274200	Enhancers	Fetal Thymus	thymus
7	chr4:48273200-48274000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:48273200-48274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:48273200-48277200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:48273200-48277600	Weak transcription	Fetal Intestine Large	intestine
11	chr4:48273200-48279400	Weak transcription	Primary T cells from cord blood	blood
12	chr4:48273400-48281600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:48273600-48276800	Weak transcription	K562	blood
14	chr4:48273600-48279400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:48273800-48274000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr4:48273800-48277200	Weak transcription	Thymus	Thymus
17	chr4:48273800-48281600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links