Variant report

Variant	rs1974562
Chromosome Location	chr7:97502737-97502738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1049674	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1229569	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17345286	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2394762	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28371965	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28393117	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576085	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28756005	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894138	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6966736	0.90[CEU][hapmap]
rs6967034	0.90[CEU][hapmap]
rs7793277	0.90[CEU][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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv428178	chr7:97402756-97648029	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758124	chr7:97476284-97648029	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759546	chr7:97476284-97648029	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv981552	chr7:97500692-97502806	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv16850	chr7:97502248-97578516	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1974562	PPP1R9A	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97501800-97503000	Weak transcription	Esophagus	oesophagus
2	chr7:97501800-97503200	Enhancers	Spleen	Spleen
3	chr7:97502000-97503200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:97502200-97502800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr7:97502200-97503000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr7:97502200-97503200	Enhancers	HepG2	liver
7	chr7:97502200-97504400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:97502400-97502800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr7:97502400-97502800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr7:97502400-97502800	Enhancers	K562	blood
11	chr7:97502400-97503000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr7:97502400-97503200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr7:97502600-97502800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
14	chr7:97502600-97502800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr7:97502600-97503000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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