Variant report

Variant	rs28741391
Chromosome Location	chr3:53884416-53884417
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	POLR2A	chr3:53881915-53884827	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53879984..53882560-chr3:53883892..53885609,2	K562	blood:
2	chr3:53882268..53884684-chr3:53906455..53909246,2	MCF-7	breast:

Variant related genes	Relation type
CHDH	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000056736	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2276839	0.95[ASN][1000 genomes]
rs28385740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28741390	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73841203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73843331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53881000-53885200	Weak transcription	Right Atrium	heart
2	chr3:53881000-53892600	Weak transcription	Psoas Muscle	Psoas
3	chr3:53881000-53893200	Weak transcription	Ovary	ovary
4	chr3:53881200-53892400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:53881200-53895000	Weak transcription	A549	lung
6	chr3:53881200-53895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53881400-53886600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:53881400-53887000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:53881400-53887200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53881400-53887400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:53881400-53889200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:53881400-53891400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:53881400-53892000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:53881400-53892000	Weak transcription	Gastric	stomach
15	chr3:53881400-53892200	Weak transcription	Fetal Intestine Large	intestine
16	chr3:53881400-53892200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:53881400-53892600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:53881400-53892600	Weak transcription	Hela-S3	cervix
19	chr3:53881400-53892800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:53881400-53893000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:53881400-53893000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:53881600-53887000	Weak transcription	Liver	Liver
23	chr3:53882400-53886800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:53882400-53891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:53882600-53886200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:53882600-53892200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:53882800-53886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:53882800-53892200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:53883000-53891000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:53883200-53887600	Weak transcription	Pancreas	Pancrea
31	chr3:53883200-53889400	Weak transcription	GM12878-XiMat	blood
32	chr3:53884000-53887600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:53884000-53895800	Strong transcription	HepG2	liver
34	chr3:53884400-53884800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:53884400-53885200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:53884400-53892200	Weak transcription	Fetal Brain Female	brain
37	chr3:53884400-53892800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links