Variant report

Variant	rs6873987
Chromosome Location	chr5:75443228-75443229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75441859..75445534-chr5:75469171..75472141,3	K562	blood:

Variant related genes	Relation type
ENSG00000254893	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10066377	0.85[CEU][hapmap]
rs10805897	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942754	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10942756	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10942757	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742697	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11743217	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514991	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522618	0.85[CEU][hapmap]
rs12523629	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12659363	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs17746851	0.83[CHB][hapmap]
rs17747008	0.90[ASN][1000 genomes]
rs1862521	0.80[ASN][1000 genomes]
rs1895390	0.84[CEU][hapmap]
rs1895391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336686	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709896	0.90[ASN][1000 genomes]
rs34064105	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34253050	0.90[ASN][1000 genomes]
rs35683245	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277896	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4296783	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4566769	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610441	0.85[CEU][hapmap]
rs56279201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57791510	0.99[ASN][1000 genomes]
rs62361382	0.92[EUR][1000 genomes]
rs62363488	0.85[EUR][1000 genomes]
rs62363490	0.87[EUR][1000 genomes]
rs6453208	0.81[YRI][hapmap]
rs6866404	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs6886779	0.93[ASN][1000 genomes]
rs6887382	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736005	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7709175	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7716284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723492	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732994	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734441	0.89[EUR][1000 genomes]
rs7736875	0.87[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	esv34707	chr5:75429015-75450144	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1021722	chr5:75429015-75450547	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	nsv1019869	chr5:75431439-75446612	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv818353	chr5:75431439-75450127	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1018966	chr5:75431439-75450547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv2763917	chr5:75431439-75450559	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv516875	chr5:75431439-75455251	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv598677	chr5:75431439-75455251	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1033837	chr5:75432737-75450547	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv1021628	chr5:75435313-75450547	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1015349	chr5:75439222-75450132	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6873987	FCHO2	cis	parietal	SCAN
rs6873987	METTL7A	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75442200-75449800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:75443200-75443400	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:75443200-75443400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:75443200-75443400	Enhancers	Pancreas	Pancrea
5	chr5:75443200-75445400	Enhancers	Ovary	ovary

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