Variant report

Variant	rs2254468
Chromosome Location	chr9:16804197-16804198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10733321	1.00[JPT][hapmap]
rs10810618	1.00[JPT][hapmap]
rs10810623	1.00[JPT][hapmap]
rs10810632	1.00[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs13289196	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1330300	1.00[JPT][hapmap]
rs1537002	1.00[JPT][hapmap]
rs17743593	0.85[CEU][hapmap]
rs2026803	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2243614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2243719	0.87[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2243836	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2254193	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2480924	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2812002	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3927535	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4961495	1.00[JPT][hapmap]
rs4961760	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[AMR][1000 genomes]
rs6475071	1.00[JPT][hapmap]
rs6475081	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6475082	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7037653	1.00[JPT][hapmap]
rs73649035	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7850168	1.00[JPT][hapmap]
rs7859111	1.00[JPT][hapmap]
rs7873181	1.00[JPT][hapmap]
rs9407777	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2254468	CD44	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16796200-16810400	Weak transcription	HSMM	muscle
2	chr9:16796200-16813400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:16796200-16816800	Weak transcription	HSMMtube	muscle
4	chr9:16796400-16824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:16796600-16809000	Weak transcription	Osteobl	bone
6	chr9:16798000-16809600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:16799200-16813200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:16801400-16805000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:16801600-16805400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:16801800-16804800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr9:16802000-16804600	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:16802000-16804600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:16802200-16804600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr9:16802200-16804600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:16802200-16804800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:16802600-16804600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:16802600-16807000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:16802800-16810000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:16802800-16811800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:16803200-16804600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr9:16803200-16809200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:16803400-16806000	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:16803400-16809600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:16803600-16804400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:16803600-16805600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:16803800-16804400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr9:16803800-16807000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:16803800-16811800	Weak transcription	NHLF	lung
29	chr9:16804000-16804400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:16804000-16811800	Weak transcription	Fetal Stomach	stomach
31	chr9:16804000-16812000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links