Variant report

Variant	rs2817688
Chromosome Location	chr10:98850800-98850801
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11189001	0.89[JPT][hapmap]
rs11189002	0.92[JPT][hapmap]
rs12268671	0.90[JPT][hapmap]
rs12572597	0.80[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12782356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17112401	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2636796	0.81[CEU][hapmap]
rs2805603	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2805604	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2817685	0.84[JPT][hapmap]
rs2817686	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2861828	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2861829	0.99[ASN][1000 genomes]
rs902471	0.83[ASN][1000 genomes]
rs937074	0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv2758236	chr10:98789963-98962472	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv2759777	chr10:98789963-98962472	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1037576	chr10:98791099-98873649	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1039568	chr10:98800844-98868329	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1040262	chr10:98805336-98872134	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2817688	FRAT1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98841200-98869200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:98847400-98855200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr10:98847400-98860600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:98847600-98855400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr10:98848200-98856400	Weak transcription	Thymus	Thymus
6	chr10:98848800-98852400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr10:98848800-98855000	Weak transcription	Brain Germinal Matrix	brain
8	chr10:98849000-98855600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:98850000-98853200	Strong transcription	Fetal Thymus	thymus
10	chr10:98850000-98854200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:98850000-98855200	Weak transcription	Brain Anterior Caudate	brain
12	chr10:98850000-98855400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:98850000-98855400	Weak transcription	Right Atrium	heart

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Input of quick search could be:

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

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