Variant report

Variant	rs1409633
Chromosome Location	chr9:12771869-12771870
allele	C/T
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	FOS	chr9:12771829-12772315	MCF10A-Er-Src	breast:	n/a	n/a
2	BHLHE40	chr9:12771808-12772164	A549	lung:	n/a	n/a
3	STAT3	chr9:12771852-12772254	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr9:12771834-12772163	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12770939..12774696-chr9:12774747..12779041,5	MCF-7	breast:
2	chr9:12771458..12774120-chr9:12775878..12777874,2	K562	blood:

Variant related genes	Relation type
LURAP1L	TF binding region
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10115741	0.86[EUR][1000 genomes]
rs1041175	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10733246	0.89[EUR][1000 genomes]
rs10733247	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1074790	0.93[CHB][hapmap];0.80[CHD][hapmap]
rs10756408	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10809830	0.84[ASN][1000 genomes]
rs10809838	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10960780	0.84[ASN][1000 genomes]
rs10960786	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326779	0.80[CHD][hapmap]
rs1326781	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1326794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1326796	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1409631	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1854022	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1887175	0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1887176	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1887177	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs2147249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2181816	0.93[CHB][hapmap]
rs2209273	0.93[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs2209274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2382362	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2382363	0.86[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2382364	0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2382368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4996096	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6474729	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7019486	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs7019694	0.92[EUR][1000 genomes]
rs7019981	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs7025099	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025475	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7037828	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7039957	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7049095	0.93[ASN][1000 genomes]
rs7859275	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9696885	0.85[ASN][1000 genomes]
rs992652	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12761600-12774800	Weak transcription	NHLF	lung
2	chr9:12765400-12772000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:12766800-12774800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:12766800-12774800	Weak transcription	HSMMtube	muscle
5	chr9:12770400-12774800	Weak transcription	Fetal Intestine Small	intestine
6	chr9:12770600-12774800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:12771000-12772000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:12771000-12773000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:12771400-12774800	Weak transcription	Fetal Intestine Large	intestine
10	chr9:12771600-12773200	Enhancers	HMEC	breast
11	chr9:12771800-12772200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:12771800-12772200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:12771800-12772400	Enhancers	HUVEC	blood vessel
14	chr9:12771800-12772600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:12771800-12772600	Enhancers	Osteobl	bone
16	chr9:12771800-12772800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:12771800-12772800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:12771800-12772800	Enhancers	A549	lung
19	chr9:12771800-12772800	Enhancers	HSMM	muscle
20	chr9:12771800-12772800	Enhancers	NH-A	brain
21	chr9:12771800-12772800	Flanking Active TSS	NHEK	skin
22	chr9:12771800-12773000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:12771800-12773000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:12771800-12773000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:12771800-12773200	Enhancers	NHDF-Ad	bronchial
26	chr9:12771800-12773800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:12771800-12773800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:12771800-12774000	Enhancers	Fetal Lung	lung
29	chr9:12771800-12774600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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