Variant report

Variant	rs6879785
Chromosome Location	chr5:75450373-75450374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10066725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10072459	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs11955072	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12657276	0.83[CEU][hapmap]
rs1559203	0.82[JPT][hapmap]
rs2059156	1.00[ASN][1000 genomes]
rs2059157	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs28581866	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4299714	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs4371731	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6453203	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6879305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6889023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs6897128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6897302	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6898301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6898618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs71585074	0.85[ASN][1000 genomes]
rs7726643	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1034853	chr5:75382047-75534981	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv462212	chr5:75388834-75534570	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv598676	chr5:75388834-75534570	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv526084	chr5:75410511-75530494	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2757119	chr5:75426863-75474780	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv2759351	chr5:75426863-75474780	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1021722	chr5:75429015-75450547	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv34958	chr5:75429015-75474921	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1018966	chr5:75431439-75450547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv2763917	chr5:75431439-75450559	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv516875	chr5:75431439-75455251	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv598677	chr5:75431439-75455251	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1033837	chr5:75432737-75450547	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1021628	chr5:75435313-75450547	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6879785	AGGF1	cis	parietal	SCAN
rs6879785	FCHO2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75449800-75450600	Enhancers	H9 Cell Line	embryonic stem cell
2	chr5:75449800-75450600	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:75450000-75450400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:75450200-75451000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:75450200-75451200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:75450200-75451400	Enhancers	HUES48 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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