Variant report

Variant	rs12199428
Chromosome Location	chr6:114662065-114662066
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	chr6:114655643..114657954-chr6:114659786..114662441,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1028300	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456892	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457275	0.92[EUR][1000 genomes]
rs10457276	0.92[EUR][1000 genomes]
rs10457277	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457278	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457279	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153478	0.92[EUR][1000 genomes]
rs11153480	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754047	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756498	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189772	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190227	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190524	1.00[ASN][1000 genomes]
rs12190621	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192586	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192949	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194343	1.00[ASN][1000 genomes]
rs12194780	1.00[ASN][1000 genomes]
rs12196148	1.00[ASN][1000 genomes]
rs12196343	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196684	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196717	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197768	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199067	1.00[ASN][1000 genomes]
rs12202564	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203102	1.00[ASN][1000 genomes]
rs12203297	1.00[ASN][1000 genomes]
rs12203473	1.00[ASN][1000 genomes]
rs12203936	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206111	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206217	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207904	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207919	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208021	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211634	1.00[ASN][1000 genomes]
rs12211637	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212330	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212361	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214339	1.00[ASN][1000 genomes]
rs12215919	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216093	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191892	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196504	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210832	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211232	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211367	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211773	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214864	1.00[ASN][1000 genomes]
rs1337333	1.00[ASN][1000 genomes]
rs1415427	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17076088	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34144978	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35103890	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35633522	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713770	1.00[ASN][1000 genomes]
rs35898688	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56147035	0.89[AFR][1000 genomes]
rs56171501	0.89[AFR][1000 genomes]
rs58800329	0.89[AFR][1000 genomes]
rs58973977	0.89[AFR][1000 genomes]
rs61094271	0.89[AFR][1000 genomes]
rs6568837	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66605950	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66786400	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68097954	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899884	0.89[AFR][1000 genomes]
rs6900928	0.89[AFR][1000 genomes]
rs6923441	0.89[AFR][1000 genomes]
rs71566768	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71566769	1.00[ASN][1000 genomes]
rs73544441	0.89[AFR][1000 genomes]
rs73544443	0.89[AFR][1000 genomes]
rs73544448	0.82[AFR][1000 genomes]
rs73544451	0.89[AFR][1000 genomes]
rs73544455	0.89[AFR][1000 genomes]
rs73544456	0.89[AFR][1000 genomes]
rs73546536	1.00[ASN][1000 genomes]
rs7755266	0.85[AFR][1000 genomes]
rs7772400	0.89[AFR][1000 genomes]
rs9384899	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481447	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688966	1.00[ASN][1000 genomes]
rs9689766	1.00[ASN][1000 genomes]
rs9689797	0.89[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	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv464024	chr6:114489321-114837181	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv604544	chr6:114489321-114837181	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3692910	chr6:114597419-115480580	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv528128	chr6:114597657-115471129	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv818451	chr6:114597657-115471129	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114659800-114665400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:114660600-114662400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr6:114660600-114662600	Active TSS	Fetal Brain Female	brain
4	chr6:114661000-114662400	Active TSS	HepG2	liver
5	chr6:114661000-114665000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:114661000-114665200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:114661000-114665800	Active TSS	Brain Anterior Caudate	brain
8	chr6:114661200-114662200	Weak transcription	Brain Germinal Matrix	brain
9	chr6:114661200-114662400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:114661200-114662400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:114661200-114665000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:114661200-114665200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:114661400-114662200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:114661400-114662200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:114661400-114665200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr6:114661400-114665400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:114661400-114665600	Active TSS	Brain Angular Gyrus	brain
18	chr6:114661600-114662200	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:114661600-114662400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:114661600-114665000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:114661600-114665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:114661800-114662200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:114661800-114662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:114661800-114662600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:114661800-114662600	Weak transcription	HSMM	muscle
26	chr6:114661800-114662800	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:114661800-114665000	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:114662000-114662200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:114662000-114662200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr6:114662000-114662200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:114662000-114662400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:114662000-114663400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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