Variant report

Variant	rs548348
Chromosome Location	chr9:97354528-97354529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1042144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821376	0.83[EUR][1000 genomes]
rs10993275	0.87[CEU][hapmap];0.82[CHB][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs10993277	0.83[EUR][1000 genomes]
rs10993278	0.85[EUR][1000 genomes]
rs12238876	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13284668	0.87[EUR][1000 genomes]
rs13291835	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13296485	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16937175	0.91[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1754435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1754439	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999122	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2017136	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2296708	0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs2679599	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679600	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679602	0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2772022	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790390	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369670	0.84[EUR][1000 genomes]
rs2945802	0.84[TSI][hapmap]
rs2987882	0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2987897	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993905	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2993912	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2993958	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993959	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993961	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993962	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3824484	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3896183	0.83[EUR][1000 genomes]
rs4075984	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743961	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4744362	0.91[CEU][hapmap];0.82[CHB][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs479197	0.84[EUR][1000 genomes]
rs514222	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs515339	0.89[EUR][1000 genomes]
rs540124	0.81[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs547834	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576745	0.87[CEU][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs583365	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632506	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67721291	0.87[EUR][1000 genomes]
rs693399	0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs802918	0.86[EUR][1000 genomes]
rs8192689	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs874248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9695	0.83[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
2	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs548348	HIATL1	cis	parietal	SCAN
rs548348	PHF2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97351800-97369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97353800-97354600	Enhancers	Stomach Mucosa	stomach
4	chr9:97354000-97354600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr9:97354200-97354600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr9:97354200-97354800	Enhancers	Duodenum Mucosa	Duodenum
7	chr9:97354400-97354600	Enhancers	Gastric	stomach
8	chr9:97354400-97355600	Weak transcription	Psoas Muscle	Psoas

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