Variant report

Variant	rs4744566
Chromosome Location	chr9:71955175-71955176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71950254..71952717-chr9:71953240..71956144,4	MCF-7	breast:
2	chr9:71938069..71941613-chr9:71952585..71956255,4	MCF-7	breast:
3	chr9:71954955..71956543-chr9:71958327..71960224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10735537	0.98[ASN][1000 genomes]
rs10735538	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867357	0.82[CHD][hapmap]
rs10867360	0.83[AMR][1000 genomes]
rs10867367	0.82[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs11791211	0.82[ASN][1000 genomes]
rs13287458	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13292207	0.83[AMR][1000 genomes]
rs1339544	0.87[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1931555	0.98[ASN][1000 genomes]
rs3934321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4237229	0.98[ASN][1000 genomes]
rs4341224	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4382537	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4515616	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4537363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744881	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6559478	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6559480	0.91[ASN][1000 genomes]
rs7021089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027671	0.85[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7028837	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033121	0.98[ASN][1000 genomes]
rs7043840	0.98[ASN][1000 genomes]
rs7044101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7045431	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713186	0.86[AFR][1000 genomes]
rs72713188	0.85[AFR][1000 genomes]
rs7852930	0.83[AMR][1000 genomes]
rs7861213	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7868245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7875734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4744566	TJP2	cis	parietal	SCAN
rs4744566	C9orf57	cis	cerebellum	SCAN
rs4744566	FAM189A2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71947000-71958000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:71947200-71962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:71948800-71962000	Weak transcription	Pancreas	Pancrea
4	chr9:71950600-71959400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:71950800-71959400	Weak transcription	Lung	lung
6	chr9:71951600-71955200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:71952200-71956200	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:71952800-71955400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:71953600-71955400	Enhancers	Fetal Heart	heart
10	chr9:71954200-71955800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr9:71954200-71956200	Enhancers	Ovary	ovary
12	chr9:71954400-71955200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:71954400-71955400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr9:71954400-71955400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:71954400-71955600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr9:71954400-71955600	Enhancers	Left Ventricle	heart
17	chr9:71954400-71955600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:71954600-71955400	Enhancers	H9 Cell Line	embryonic stem cell
19	chr9:71954600-71955600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:71954600-71955600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:71954800-71955400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:71954800-71955400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:71954800-71955600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:71954800-71957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:71955000-71955200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:71955000-71956000	Weak transcription	Psoas Muscle	Psoas
27	chr9:71955000-71957600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:71955000-71957600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:71955000-71959200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:71955000-71959400	Weak transcription	Right Atrium	heart
31	chr9:71955000-71961600	Weak transcription	Right Ventricle	heart
32	chr9:71955000-71961800	Weak transcription	HMEC	breast
33	chr9:71955000-71962000	Weak transcription	Gastric	stomach

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