Variant report

Variant	rs7440590
Chromosome Location	chr4:90028412-90028413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:90026718..90029366-chr4:90030525..90032807,2	MCF-7	breast:
2	chr4:90026203..90028605-chr4:90033601..90036574,2	K562	blood:
3	chr4:89442768..89444878-chr4:90027120..90029163,2	K562	blood:

Variant related genes	Relation type
ENSG00000271359	Chromatin interaction
ENSG00000180346	Chromatin interaction
ENSG00000255072	Chromatin interaction
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10009665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097214	0.94[ASN][1000 genomes]
rs11097215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641645	0.88[ASN][1000 genomes]
rs12643834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644568	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646713	0.94[ASN][1000 genomes]
rs12646734	0.94[ASN][1000 genomes]
rs13124770	0.94[ASN][1000 genomes]
rs13148714	0.88[ASN][1000 genomes]
rs1355835	0.88[ASN][1000 genomes]
rs1355838	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1513807	0.82[CEU][hapmap]
rs1513821	0.87[ASN][1000 genomes]
rs1533291	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs17015025	0.82[CHD][hapmap]
rs1708661	0.89[JPT][hapmap]
rs1708674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1708678	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs1708684	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs1795721	0.87[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1795731	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1795732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1795733	0.83[CEU][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs2037036	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037037	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280099	0.82[CHD][hapmap]
rs2458545	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2458546	0.80[ASN][1000 genomes]
rs2458547	0.80[ASN][1000 genomes]
rs2464517	0.87[ASN][1000 genomes]
rs2670624	0.83[CEU][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs2670625	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2670626	0.83[CEU][hapmap];0.89[JPT][hapmap];0.88[TSI][hapmap]
rs2670629	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs2670630	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs2704597	0.87[ASN][1000 genomes]
rs2869987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869990	0.88[ASN][1000 genomes]
rs4634189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693221	0.84[ASN][1000 genomes]
rs4693983	0.90[ASN][1000 genomes]
rs6532094	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs6532099	0.83[ASN][1000 genomes]
rs6532109	0.86[ASN][1000 genomes]
rs6532112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833401	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6833424	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833576	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835031	0.90[ASN][1000 genomes]
rs6844490	0.89[JPT][hapmap]
rs6854285	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665891	0.87[ASN][1000 genomes]
rs756175	0.90[ASN][1000 genomes]
rs756176	0.90[ASN][1000 genomes]
rs7660709	0.92[GIH][hapmap]
rs7691983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938264	0.90[ASN][1000 genomes]
rs938268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991151	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7440590	FAM190A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90017200-90031600	Weak transcription	Right Atrium	heart
2	chr4:90021000-90029800	Weak transcription	Primary T cells from cord blood	blood
3	chr4:90024200-90031800	Weak transcription	Aorta	Aorta
4	chr4:90027800-90028600	Enhancers	Right Ventricle	heart
5	chr4:90028400-90030800	Enhancers	Pancreas	Pancrea
6	chr4:90028400-90031200	Weak transcription	Ovary	ovary

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