Variant report

Variant	rs12027872
Chromosome Location	chr1:225836119-225836120
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	chr1:225821003..225822797-chr1:225833580..225836566,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10429871	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11801322	0.88[EUR][1000 genomes]
rs12033453	0.92[ASN][1000 genomes]
rs12038461	0.82[ASN][1000 genomes]
rs12038893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12039453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043837	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs1340868	1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs1537877	1.00[AFR][1000 genomes]
rs1537878	1.00[AFR][1000 genomes]
rs16845078	1.00[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs16845153	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap]
rs17500562	1.00[AFR][1000 genomes]
rs17500604	1.00[AFR][1000 genomes]
rs17500639	1.00[AFR][1000 genomes]
rs17500679	1.00[AFR][1000 genomes]
rs17500814	1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs17500944	1.00[AFR][1000 genomes]
rs17501138	0.86[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs17501249	1.00[AFR][1000 genomes]
rs17501775	1.00[AFR][1000 genomes]
rs17501845	1.00[AFR][1000 genomes]
rs17501956	0.86[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs17502068	0.86[GIH][hapmap];1.00[TSI][hapmap]
rs17502075	1.00[AFR][1000 genomes]
rs17502774	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17502823	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17502858	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17502961	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17503792	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17559267	1.00[AFR][1000 genomes]
rs17559587	1.00[TSI][hapmap];1.00[AFR][1000 genomes]
rs17560021	1.00[AFR][1000 genomes]
rs17560579	1.00[AFR][1000 genomes]
rs17561095	1.00[AFR][1000 genomes]
rs17561228	1.00[AFR][1000 genomes]
rs17561368	1.00[AFR][1000 genomes]
rs17561781	0.84[EUR][1000 genomes]
rs17562010	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17562052	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17568665	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17569049	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17569145	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1832229	1.00[AFR][1000 genomes]
rs1870834	0.81[ASN][1000 genomes]
rs1876085	1.00[AFR][1000 genomes]
rs1876086	0.86[GIH][hapmap];1.00[TSI][hapmap]
rs28617210	0.88[EUR][1000 genomes]
rs3947140	1.00[AFR][1000 genomes]
rs56793390	0.89[ASN][1000 genomes]
rs6687755	0.88[EUR][1000 genomes]
rs73125707	0.86[EUR][1000 genomes]
rs74147627	0.81[ASN][1000 genomes]
rs954615	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[EUR][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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
3	chr1:225813800-225838600	Weak transcription	HMEC	breast
4	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
7	chr1:225816200-225836600	Weak transcription	Adipose Nuclei	Adipose
8	chr1:225819600-225836400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:225820800-225837200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:225823800-225836600	Weak transcription	NHLF	lung
11	chr1:225825000-225837400	Weak transcription	Hela-S3	cervix
12	chr1:225825600-225839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:225825800-225837200	Weak transcription	NHEK	skin
14	chr1:225826200-225838800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:225826200-225839400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:225828600-225836200	Weak transcription	Right Atrium	heart
17	chr1:225830200-225836600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:225830200-225838800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:225830400-225836600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:225830400-225836600	Weak transcription	Right Ventricle	heart
21	chr1:225830400-225838200	Weak transcription	Pancreas	Pancrea
22	chr1:225830400-225839200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:225830400-225839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:225830400-225839600	Weak transcription	Gastric	stomach
25	chr1:225831400-225836200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:225831600-225836600	Weak transcription	Fetal Stomach	stomach
27	chr1:225831600-225837600	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:225831600-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:225832400-225838200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:225832800-225836600	Weak transcription	NHDF-Ad	bronchial
31	chr1:225833000-225838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:225833200-225836200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:225833200-225836200	Weak transcription	NH-A	brain
34	chr1:225833200-225837200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225833200-225838200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:225833400-225836600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:225833400-225836600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:225833600-225836200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:225833600-225836400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:225833800-225836800	Weak transcription	Fetal Brain Female	brain
41	chr1:225833800-225836800	Enhancers	Fetal Lung	lung
42	chr1:225834000-225836400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:225834200-225836200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:225834200-225839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:225834400-225836600	Weak transcription	Ovary	ovary
46	chr1:225834400-225837000	Weak transcription	Psoas Muscle	Psoas
47	chr1:225834400-225838200	Weak transcription	Left Ventricle	heart
48	chr1:225834600-225837800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:225834800-225837400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:225834800-225837600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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