Variant report

Variant	rs6841431
Chromosome Location	chr4:91116156-91116157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:91048424..91050386-chr4:91115679..91118506,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184305	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10013445	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs12647157	0.81[ASW][hapmap];0.91[CEU][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[TSI][hapmap]
rs12647859	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.80[EUR][1000 genomes]
rs17016701	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs17016715	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1903575	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35994777	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4356886	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57438794	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57957708	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60027158	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60211684	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60534314	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6812983	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6813238	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847189	0.95[JPT][hapmap]
rs73832739	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73832741	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73832743	0.80[EUR][1000 genomes]
rs7693009	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830006	chr4:90971656-91186340	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv1007826	chr4:91049593-91438961	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv537177	chr4:91049593-91438961	Bivalent/Poised TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv999065	chr4:91049593-91520073	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6841431	FAM190A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91109200-91117200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:91109200-91118800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:91109400-91119000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:91111600-91116200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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