Variant report

Variant	rs12205460
Chromosome Location	chr6:144894672-144894673
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144893219..144895827-chr6:144896800..144899296,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10080939	0.93[EUR][1000 genomes]
rs10447422	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10457764	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10499230	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11155359	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12190718	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12192622	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12200263	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12202539	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12204734	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12209699	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12209889	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17073869	0.90[EUR][1000 genomes]
rs17793570	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1918749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28588721	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34810766	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4460225	0.90[EUR][1000 genomes]
rs4615409	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56264877	0.90[EUR][1000 genomes]
rs60530618	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6917268	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917519	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6923281	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6942069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73600166	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73600170	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73603015	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773603	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
2	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:144857200-144904000	Weak transcription	Psoas Muscle	Psoas
7	chr6:144864800-144899000	Weak transcription	Small Intestine	intestine
8	chr6:144867400-144903800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:144870800-144898400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:144872000-144903000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:144873000-144903200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:144873000-144903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:144874000-144904200	Weak transcription	Placenta	Placenta
14	chr6:144877000-144895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:144877000-144898000	Weak transcription	Right Ventricle	heart
16	chr6:144877000-144898200	Weak transcription	Fetal Intestine Small	intestine
17	chr6:144877000-144903000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:144877000-144904200	Weak transcription	Fetal Stomach	stomach
19	chr6:144878000-144903400	Weak transcription	Fetal Brain Male	brain
20	chr6:144878400-144898000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:144878400-144899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:144878600-144898000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:144878600-144898200	Weak transcription	Lung	lung
24	chr6:144878600-144901200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:144878800-144898000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:144879000-144898000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:144879000-144898200	Weak transcription	Esophagus	oesophagus
28	chr6:144879000-144898200	Weak transcription	Fetal Intestine Large	intestine
29	chr6:144879000-144898200	Weak transcription	Spleen	Spleen
30	chr6:144879000-144898200	Weak transcription	GM12878-XiMat	blood
31	chr6:144879200-144898800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:144879200-144899800	Weak transcription	NHLF	lung
33	chr6:144879200-144904000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:144879600-144898000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:144879600-144898200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:144879600-144898200	Weak transcription	NHDF-Ad	bronchial
37	chr6:144881400-144898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:144881600-144895200	Weak transcription	NHEK	skin
39	chr6:144881600-144895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:144881600-144899200	Weak transcription	HSMMtube	muscle
41	chr6:144881800-144895000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:144881800-144898200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:144881800-144898200	Weak transcription	Gastric	stomach
44	chr6:144881800-144899600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:144881800-144900000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:144881800-144937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:144882000-144902800	Weak transcription	Fetal Heart	heart
48	chr6:144883800-144898200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:144884000-144898200	Weak transcription	Fetal Lung	lung
50	chr6:144884600-144898000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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