Variant report

Variant	rs10756402
Chromosome Location	chr9:12739948-12739949
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12737180..12738894-chr9:12739213..12741322,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10115741	0.83[ASN][1000 genomes]
rs10120165	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10123986	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10124197	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733246	0.84[ASN][1000 genomes]
rs10733247	0.81[ASN][1000 genomes]
rs10738290	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1074789	0.90[YRI][hapmap]
rs1074790	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10756399	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10756400	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756401	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10756406	0.93[YRI][hapmap]
rs10809830	0.90[ASN][1000 genomes]
rs10809838	0.85[CHB][hapmap]
rs10960776	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10960780	0.80[AMR][1000 genomes]
rs12342045	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1326779	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1326780	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326781	0.84[ASN][1000 genomes]
rs1326794	0.85[CHB][hapmap]
rs1326796	0.85[CHB][hapmap]
rs1409633	0.85[CHB][hapmap]
rs1543587	0.93[YRI][hapmap]
rs1854022	0.90[ASN][1000 genomes]
rs2147249	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2181816	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2209274	0.86[CHB][hapmap]
rs2382362	0.84[ASN][1000 genomes]
rs2382363	0.93[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2382364	0.93[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2382365	0.96[ASN][1000 genomes]
rs2382368	0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2890965	0.81[AFR][1000 genomes]
rs4741245	0.97[YRI][hapmap]
rs4996096	0.81[ASN][1000 genomes]
rs6474728	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6474729	0.89[ASN][1000 genomes]
rs7019486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7019890	0.84[ASN][1000 genomes]
rs7019981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7028587	0.81[AFR][1000 genomes]
rs7035500	0.93[YRI][hapmap]
rs7039957	0.85[CHB][hapmap]
rs7044022	0.81[AFR][1000 genomes]
rs7047704	0.96[ASN][1000 genomes]
rs7048117	0.96[ASN][1000 genomes]
rs7850079	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7871257	0.85[CHB][hapmap]
rs927868	0.97[YRI][hapmap]
rs927869	0.96[YRI][hapmap]
rs970944	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs970945	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs970946	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs970947	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs992652	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
12	nsv8420	chr9:12725200-12750151	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3693020	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv818690	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	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
16	nsv516527	chr9:12738690-12748486	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 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	chr9:12737600-12741000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:12737800-12741200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:12739000-12741200	Enhancers	HMEC	breast
5	chr9:12739200-12740200	Weak transcription	Fetal Lung	lung
6	chr9:12739200-12741000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr9:12739200-12741400	Enhancers	NHEK	skin
8	chr9:12739400-12740000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:12739400-12740800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:12739600-12740000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:12739600-12740600	Weak transcription	Osteobl	bone
12	chr9:12739600-12740800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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