Variant report

Variant	rs1412297
Chromosome Location	chr9:12933637-12933638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12922589..12925309-chr9:12932316..12933934,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10738300	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332056	0.85[ASN][1000 genomes]
rs1332057	0.90[ASN][1000 genomes]
rs1332058	0.90[ASN][1000 genomes]
rs1332059	0.90[ASN][1000 genomes]
rs1332060	0.90[ASN][1000 genomes]
rs1332061	0.90[ASN][1000 genomes]
rs1412296	0.87[ASN][1000 genomes]
rs16929942	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1819460	0.90[ASN][1000 genomes]
rs1888860	0.90[ASN][1000 genomes]
rs1929916	0.87[ASN][1000 genomes]
rs1929917	0.90[ASN][1000 genomes]
rs1953022	0.90[ASN][1000 genomes]
rs1953023	0.90[ASN][1000 genomes]
rs2095036	0.90[ASN][1000 genomes]
rs2104876	0.89[ASN][1000 genomes]
rs2382377	0.90[ASN][1000 genomes]
rs2382378	0.90[ASN][1000 genomes]
rs2382379	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35270390	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55746363	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56042324	0.84[AMR][1000 genomes]
rs57009769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029508	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7035514	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038912	0.90[ASN][1000 genomes]
rs7043940	0.81[AMR][1000 genomes]
rs7854690	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs868338	0.90[ASN][1000 genomes]
rs883093	0.89[ASN][1000 genomes]
rs885132	0.90[ASN][1000 genomes]
rs885133	0.91[ASN][1000 genomes]
rs944620	0.89[ASN][1000 genomes]
rs944621	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv613616	chr9:12922330-13018096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv892576	chr9:12925921-13093345	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv466258	chr9:12928475-12968196	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv613617	chr9:12928475-12968196	Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv892577	chr9:12928475-12995112	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12917200-12934000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr9:12924800-12933800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:12925400-12934200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:12931000-12934000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:12931200-12933800	Weak transcription	NHEK	skin
6	chr9:12931200-12934000	Weak transcription	Osteobl	bone
7	chr9:12932200-12934000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:12932200-12934000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:12932200-12934000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:12932400-12934400	Enhancers	HUVEC	blood vessel
11	chr9:12932600-12934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:12933200-12934800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:12933200-12936000	Enhancers	NHDF-Ad	bronchial
14	chr9:12933200-12936600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr9:12933400-12934200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:12933400-12935200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:12933400-12935400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:12933400-12936000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:12933400-12936200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:12933400-12936200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:12933400-12936800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:12933600-12933800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr9:12933600-12934800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr9:12933600-12934800	Enhancers	A549	lung
25	chr9:12933600-12934800	Enhancers	NHLF	lung
26	chr9:12933600-12936600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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