Variant report

Variant	rs4744880
Chromosome Location	chr9:71961757-71961758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71938497..71941433-chr9:71956762..71962911,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10735537	0.99[ASN][1000 genomes]
rs10735538	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10867360	0.83[AMR][1000 genomes]
rs10867367	0.83[AMR][1000 genomes]
rs11791211	0.80[ASN][1000 genomes]
rs13287458	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13292207	0.83[AMR][1000 genomes]
rs1339544	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1931555	0.99[ASN][1000 genomes]
rs3934321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4237229	0.99[ASN][1000 genomes]
rs4341224	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4382537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4537363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744566	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]
rs4744879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559480	0.93[ASN][1000 genomes]
rs7021089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027671	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7028837	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033121	0.99[ASN][1000 genomes]
rs7043840	0.99[ASN][1000 genomes]
rs7044101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7045431	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852930	0.83[AMR][1000 genomes]
rs7861213	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7868245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7875734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71947200-71962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:71948800-71962000	Weak transcription	Pancreas	Pancrea
3	chr9:71955000-71961800	Weak transcription	HMEC	breast
4	chr9:71955000-71962000	Weak transcription	Gastric	stomach
5	chr9:71955400-71981800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:71955600-71962000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr9:71958400-71962200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:71958600-71962000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:71959600-71962200	Weak transcription	Ovary	ovary
10	chr9:71959800-71961800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:71959800-71961800	Weak transcription	Left Ventricle	heart
12	chr9:71959800-71962000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:71959800-71962000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:71959800-71962000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:71959800-71962000	Weak transcription	Lung	lung
16	chr9:71959800-71962000	Weak transcription	Psoas Muscle	Psoas
17	chr9:71959800-71962000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:71961200-71963000	Enhancers	Fetal Heart	heart
19	chr9:71961400-71961800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:71961400-71962200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:71961600-71962200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:71961600-71962200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:71961600-71962200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:71961600-71962400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:71961600-71962400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr9:71961600-71962400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:71961600-71962400	Enhancers	Right Atrium	heart
28	chr9:71961600-71962400	Enhancers	Right Ventricle	heart
29	chr9:71961600-71962600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:71961600-71962600	Enhancers	NHEK	skin
31	chr9:71961600-71963200	Enhancers	HUVEC	blood vessel

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