Variant report

Variant	rs13284898
Chromosome Location	chr9:12724560-12724561
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	chr9:12723856..12726602-chr9:12884690..12886916,2	MCF-7	breast:
2	chr9:12722041..12725292-chr9:12774361..12778280,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222658	Chromatin interaction
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10491742	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10491743	1.00[ASN][1000 genomes]
rs10491744	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1063380	1.00[CHB][hapmap]
rs1074789	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs10756395	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10756405	0.83[AMR][1000 genomes]
rs10756406	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs10809826	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10809829	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10809836	1.00[ASN][1000 genomes]
rs10960758	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960759	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10960760	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10960761	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10960762	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs10960764	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10960765	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960774	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960775	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10960779	1.00[ASN][1000 genomes]
rs10960781	1.00[ASN][1000 genomes]
rs1134311	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1137134	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11789751	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11829	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12115198	0.81[AMR][1000 genomes]
rs12379024	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12379260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552462	1.00[ASN][1000 genomes]
rs1326788	1.00[ASN][1000 genomes]
rs1326789	1.00[ASN][1000 genomes]
rs1326790	1.00[ASN][1000 genomes]
rs1326791	1.00[ASN][1000 genomes]
rs1326792	1.00[ASN][1000 genomes]
rs1326797	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1326798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284453	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284467	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13288130	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13288475	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13288636	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13288681	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13289304	0.83[ASN][1000 genomes]
rs13295868	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13302551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1409626	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1409629	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1409630	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1543587	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17346161	1.00[CHB][hapmap]
rs2209269	1.00[ASN][1000 genomes]
rs2209271	1.00[ASN][1000 genomes]
rs2209277	1.00[CHB][hapmap]
rs2224863	1.00[CHB][hapmap]
rs2382361	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2733830	1.00[CHB][hapmap]
rs2733831	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap]
rs2733832	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs2733833	1.00[CHB][hapmap]
rs2733834	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2733836	1.00[CHB][hapmap]
rs2762457	0.83[AFR][1000 genomes]
rs2762458	1.00[CHB][hapmap]
rs2762460	0.83[CEU][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2762461	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2762463	1.00[CHB][hapmap]
rs2762464	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35666741	1.00[ASN][1000 genomes]
rs4741245	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7019226	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021368	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7023927	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7025678	1.00[ASN][1000 genomes]
rs7025771	1.00[ASN][1000 genomes]
rs7025812	0.82[AMR][1000 genomes]
rs7025842	1.00[ASN][1000 genomes]
rs7025914	1.00[ASN][1000 genomes]
rs7025953	1.00[ASN][1000 genomes]
rs7028587	1.00[ASN][1000 genomes]
rs7030485	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7035500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7036011	1.00[ASN][1000 genomes]
rs7039325	1.00[ASN][1000 genomes]
rs7466623	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs927868	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs927869	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs958073	1.00[CHB][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12719200-12740400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:12722600-12725000	Enhancers	A549	lung
3	chr9:12723000-12725000	Enhancers	Fetal Lung	lung
4	chr9:12723800-12726000	Weak transcription	Rectal Mucosa Donor 31	rectum

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