Variant report

Variant	rs1339544
Chromosome Location	chr9:71946358-71946359
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71938510..71941284-chr9:71942079..71947019,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10735537	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10735538	0.80[ASN][1000 genomes]
rs10780308	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10867357	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs10867360	0.89[ASN][1000 genomes]
rs10867367	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs11791211	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13292207	0.87[ASN][1000 genomes]
rs1572762	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1890634	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1931555	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3750552	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3934321	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4237229	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4382537	0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4515616	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4537363	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744566	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4744875	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744876	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4744879	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4744880	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744881	0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744882	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4744883	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6559453	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6559468	0.88[ASN][1000 genomes]
rs6559472	0.89[ASN][1000 genomes]
rs6559478	0.81[ASN][1000 genomes]
rs6559480	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7021089	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7027671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7028837	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7033121	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7040797	0.84[AMR][1000 genomes]
rs7043840	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7044101	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7045431	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7852930	0.89[ASN][1000 genomes]
rs7859876	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7861213	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7868245	0.90[CEU][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7875734	0.84[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases
6	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	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
rs1339544	FAM189A2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71941000-71946800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:71941400-71946600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:71941400-71946600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:71941400-71954400	Weak transcription	Brain Anterior Caudate	brain
5	chr9:71941600-71946600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:71941600-71946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:71941600-71946600	Weak transcription	Left Ventricle	heart
8	chr9:71941600-71946600	Weak transcription	Psoas Muscle	Psoas
9	chr9:71941600-71948600	Weak transcription	Pancreas	Pancrea
10	chr9:71941600-71950400	Weak transcription	Gastric	stomach
11	chr9:71942200-71946600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr9:71942200-71950400	Weak transcription	Lung	lung
13	chr9:71942400-71946400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr9:71942400-71950200	Weak transcription	Ovary	ovary
15	chr9:71942800-71946600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:71942800-71954400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:71943000-71946800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:71943200-71946800	Weak transcription	Right Atrium	heart
19	chr9:71943200-71954400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:71944200-71946600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:71944600-71954400	Weak transcription	Brain Substantia Nigra	brain
22	chr9:71944800-71947200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr9:71945800-71946400	Enhancers	NHEK	skin
24	chr9:71945800-71947600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr9:71946000-71946600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr9:71946000-71947400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:71946200-71946400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:71946200-71946600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:71946200-71946600	Active TSS	HMEC	breast
30	chr9:71946200-71946800	Enhancers	Fetal Heart	heart
31	chr9:71946200-71948000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr9:71946200-71948000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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