Variant report

Variant	rs16891848
Chromosome Location	chr6:39260155-39260156
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	chr6:39192543..39195270-chr6:39259985..39261560,2	K562	blood:
2	chr6:39249494..39252314-chr6:39258691..39261153,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10807204	0.84[GIH][hapmap]
rs10807205	0.88[GIH][hapmap]
rs12194951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197500	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12201021	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214300	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214342	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16891847	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395721	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap]
rs2758862	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2758875	0.87[ASN][1000 genomes]
rs2815022	0.85[ASN][1000 genomes]
rs34102522	0.89[ASN][1000 genomes]
rs34625110	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6940480	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72855524	0.89[ASN][1000 genomes]
rs9349112	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349113	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9367000	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9367001	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9367002	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9369111	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380846	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394582	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16891848	FOXP4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
3	chr6:39257800-39265800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr6:39258000-39265600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:39258600-39260800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:39258600-39262000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:39258800-39260200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr6:39258800-39260400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr6:39258800-39260800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr6:39258800-39261000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:39259000-39260200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:39259000-39260200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:39259200-39260400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:39259800-39260200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr6:39260000-39260400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
16	chr6:39260000-39260600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
17	chr6:39260000-39260600	Enhancers	Fetal Kidney	kidney
18	chr6:39260000-39260800	Enhancers	Ovary	ovary
19	chr6:39260000-39261400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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