Variant report

Variant	rs28417837
Chromosome Location	chr4:8179563-8179564
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	RAD21	chr4:8178266-8179736	SK-N-SH	brain:	n/a	chr4:8178856-8178869
2	SMC3	chr4:8178292-8179576	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8177372..8179736-chr4:8243215..8245049,2	K562	blood:
2	chr4:8158932..8160891-chr4:8178387..8181198,2	MCF-7	breast:
3	chr4:8179293..8181973-chr4:8183474..8185384,4	MCF-7	breast:
4	chr4:8178129..8181116-chr4:8187357..8190314,2	K562	blood:

Variant related genes	Relation type
SH3TC1	TF binding region
ENSG00000125089	Chromatin interaction
ENSG00000163995	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11547949	0.92[EUR][1000 genomes]
rs28370452	0.92[EUR][1000 genomes]
rs28396639	0.92[EUR][1000 genomes]
rs28398157	0.92[EUR][1000 genomes]
rs28407374	0.85[EUR][1000 genomes]
rs28480201	0.92[EUR][1000 genomes]
rs28572135	0.92[EUR][1000 genomes]
rs28580669	0.92[EUR][1000 genomes]
rs28650262	0.92[EUR][1000 genomes]
rs28716092	0.92[EUR][1000 genomes]
rs56963754	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59775110	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59829176	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73800408	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1010809	chr4:8097627-8292324	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv878593	chr4:8125788-8233341	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv461216	chr4:8154534-8276411	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv593626	chr4:8154534-8276411	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv878594	chr4:8154534-8286916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv470012	chr4:8171401-8233341	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv878596	chr4:8171401-8254784	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8170600-8183200	Weak transcription	Right Atrium	heart
2	chr4:8172400-8181600	Weak transcription	Esophagus	oesophagus
3	chr4:8176000-8190200	Weak transcription	Psoas Muscle	Psoas
4	chr4:8177400-8181000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:8178400-8179800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:8178400-8179800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr4:8178400-8179800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr4:8178400-8179800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr4:8178400-8179800	Enhancers	Fetal Muscle Leg	muscle
10	chr4:8178400-8179800	Enhancers	Fetal Thymus	thymus
11	chr4:8178400-8179800	Enhancers	Dnd41	blood
12	chr4:8178400-8180000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:8178600-8185000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:8178800-8182200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:8179000-8181600	Weak transcription	Stomach Mucosa	stomach
16	chr4:8179000-8181800	Weak transcription	Right Ventricle	heart
17	chr4:8179000-8182400	Weak transcription	Fetal Intestine Small	intestine
18	chr4:8179000-8182800	Weak transcription	Pancreas	Pancrea
19	chr4:8179200-8179600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:8179200-8179600	Weak transcription	Spleen	Spleen
21	chr4:8179200-8180200	Bivalent Enhancer	HepG2	liver
22	chr4:8179200-8180800	Weak transcription	Brain Anterior Caudate	brain
23	chr4:8179200-8182200	Weak transcription	Fetal Heart	heart
24	chr4:8179200-8182800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:8179200-8183200	Weak transcription	Left Ventricle	heart
26	chr4:8179200-8183400	Weak transcription	Thymus	Thymus
27	chr4:8179400-8179600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:8179400-8179800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:8179400-8181600	Weak transcription	Hela-S3	cervix
30	chr4:8179400-8189800	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links