Variant report

Variant	rs41754
Chromosome Location	chr7:116452892-116452893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:116339031-116340618..7:116434729-116454408	Hela-S3	cervix:
2	7:116071525-116078307..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
3	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
4	7:116434729-116454408..7:117641436-117645830	GM12878	blood:
5	7:116434729-116454408..7:116610596-116619447	H1-hESC	embryonic stem cell:	embryo
6	chr7:116451831..116454767-chr7:116457311..116458821,2	MCF-7	breast:
7	chr7:116451371..116454288-chr7:116500554..116503013,3	MCF-7	breast:
8	7:116434729-116454408..7:116782481-116788433	GM12878	blood:
9	7:116093970-116105948..7:116434729-116454408	GM12878	blood:
10	chr7:116332502..116335438-chr7:116451745..116453308,2	K562	blood:
11	7:115967532-115969617..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
12	7:116245779-116258944..7:116434729-116454408	Hela-S3	cervix:
13	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
14	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000213050	Chromatin interaction
ENSG00000198898	Chromatin interaction
ENSG00000231210	Chromatin interaction
ENSG00000234826	Chromatin interaction
ENSG00000222150	Chromatin interaction
ENSG00000243243	Chromatin interaction
ENSG00000252672	Chromatin interaction
ENSG00000105976	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000237813	Chromatin interaction
ENSG00000226367	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1356	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs28167	0.86[EUR][1000 genomes]
rs28896	0.85[EUR][1000 genomes]
rs41750	0.84[CEU][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs41758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41762	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41765	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs41770	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41773	0.86[EUR][1000 genomes]
rs41776	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs41778	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs41779	0.84[EUR][1000 genomes]
rs41781	0.84[EUR][1000 genomes]
rs41783	0.84[EUR][1000 genomes]
rs41784	0.84[EUR][1000 genomes]
rs41786	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs41791	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs41792	0.84[EUR][1000 genomes]
rs41793	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs42230	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9640774	0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41754	CTTNBP2	cis	cerebellum	SCAN
rs41754	CASP4	trans	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116448600-116453200	Enhancers	Duodenum Mucosa	Duodenum
2	chr7:116448600-116453800	Enhancers	Fetal Intestine Small	intestine
3	chr7:116448600-116454000	Enhancers	Fetal Intestine Large	intestine
4	chr7:116449200-116453400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:116449200-116453400	Weak transcription	Pancreas	Pancrea
6	chr7:116450600-116453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:116450600-116453200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:116450600-116453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:116450800-116453000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:116451000-116453200	Enhancers	Stomach Mucosa	stomach
11	chr7:116451600-116453000	Flanking Active TSS	HepG2	liver
12	chr7:116451800-116455200	Weak transcription	Adipose Nuclei	Adipose
13	chr7:116452400-116453000	Flanking Active TSS	Liver	Liver
14	chr7:116452400-116453400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:116452600-116453000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr7:116452600-116453000	Enhancers	Hela-S3	cervix
17	chr7:116452600-116453400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:116452800-116453200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:116452800-116453200	Flanking Active TSS	A549	lung
20	chr7:116452800-116453600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:116452800-116453600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr7:116452800-116456000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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