Variant report

Variant	rs6559495
Chromosome Location	chr9:71985636-71985637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:71985383-71985659	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:71985327-71985731	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr9:71985409-71985655	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr9:71985379-71985729	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr9:71985362-71985731	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr9:71985336-71985729	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr9:71985384-71985659	MCF10A-Er-Src	breast:	n/a	n/a
8	JUN	chr9:71985330-71985707	HUVEC	blood vessel:	n/a	n/a
9	FOS	chr9:71985424-71985656	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FAM189A2	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10115490	0.87[AFR][1000 genomes]
rs10118562	0.87[AFR][1000 genomes]
rs10746595	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10746596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780321	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780324	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780326	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780336	0.88[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs10867426	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10867436	0.87[AFR][1000 genomes]
rs11138304	0.83[EUR][1000 genomes]
rs11138332	0.85[EUR][1000 genomes]
rs11138334	0.84[EUR][1000 genomes]
rs11138402	0.85[AFR][1000 genomes]
rs11138412	0.83[AFR][1000 genomes]
rs1334311	0.96[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3829094	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3892193	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4112222	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4255205	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4421413	0.84[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs4458929	0.88[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs4492445	0.88[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs7047788	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851643	0.84[EUR][1000 genomes]
rs7859544	0.84[EUR][1000 genomes]
rs7870082	0.87[AFR][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	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
2	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
3	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
4	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
5	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71962200-71994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:71963200-71991800	Weak transcription	Pancreas	Pancrea
3	chr9:71972600-71991800	Weak transcription	Right Atrium	heart
4	chr9:71972800-71991400	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:71973000-71986200	Weak transcription	Stomach Mucosa	stomach
6	chr9:71977400-71992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:71978800-71987200	Weak transcription	Psoas Muscle	Psoas
8	chr9:71978800-71989200	Weak transcription	Right Ventricle	heart
9	chr9:71978800-71991600	Weak transcription	Left Ventricle	heart
10	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:71982200-71986400	Weak transcription	Ovary	ovary
12	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
13	chr9:71984600-71985800	Enhancers	Fetal Heart	heart
14	chr9:71984600-71987000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:71984800-71986200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:71984800-71986600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:71985000-71987000	Enhancers	HUVEC	blood vessel
18	chr9:71985200-71985800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr9:71985200-71985800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr9:71985200-71985800	Enhancers	Fetal Kidney	kidney
21	chr9:71985200-71986000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:71985200-71986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:71985200-71986800	Enhancers	HMEC	breast
24	chr9:71985200-71986800	Enhancers	NH-A	brain
25	chr9:71985400-71986800	Enhancers	Osteobl	bone
26	chr9:71985400-71994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:71985600-71985800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr9:71985600-71986600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:71985600-71989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:71985600-71991000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:71985600-71991200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:71985600-71991400	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:71985600-71992400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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