Variant report

Variant	rs12076466
Chromosome Location	chr1:120322054-120322055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120312850..120316176-chr1:120320921..120324121,3	MCF-7	breast:
2	chr1:120309692..120311649-chr1:120319594..120322572,2	MCF-7	breast:
3	chr1:120318567..120320764-chr1:120321980..120324094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10754419	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10923899	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10923901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12070819	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12071960	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12073231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12080486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12086303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12094770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12408507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12408976	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12409248	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2582785	0.86[JPT][hapmap]
rs28522608	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3213910	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs729233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73000454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120311800-120325400	Weak transcription	Lung	lung
3	chr1:120314400-120322600	Weak transcription	Right Atrium	heart
4	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:120316800-120322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:120316800-120322600	Weak transcription	Left Ventricle	heart
7	chr1:120316800-120322600	Weak transcription	Psoas Muscle	Psoas
8	chr1:120316800-120322600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:120316800-120326000	Weak transcription	Esophagus	oesophagus
10	chr1:120317000-120322200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:120317000-120322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:120317000-120322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:120317000-120322600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:120317000-120322600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:120317000-120322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:120317000-120322600	Weak transcription	NHEK	skin
17	chr1:120317000-120325400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:120317200-120322200	Weak transcription	Fetal Heart	heart
19	chr1:120317400-120322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:120318000-120322400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:120318400-120322400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:120318400-120322600	Weak transcription	Pancreas	Pancrea
23	chr1:120318400-120325200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:120318400-120328000	Weak transcription	Gastric	stomach
25	chr1:120320000-120322400	Weak transcription	Adipose Nuclei	Adipose
26	chr1:120321600-120322600	Enhancers	Fetal Lung	lung
27	chr1:120321600-120322800	Enhancers	A549	lung
28	chr1:120321600-120323800	Enhancers	Fetal Intestine Small	intestine
29	chr1:120321600-120330800	Enhancers	Placenta	Placenta
30	chr1:120321800-120322400	Enhancers	Stomach Mucosa	stomach
31	chr1:120321800-120322600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:120321800-120322600	Enhancers	Fetal Kidney	kidney
33	chr1:120321800-120323000	Enhancers	Fetal Intestine Large	intestine
34	chr1:120321800-120323200	Enhancers	Fetal Stomach	stomach
35	chr1:120321800-120323200	Flanking Active TSS	HepG2	liver
36	chr1:120322000-120322200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:120322000-120322400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:120322000-120322400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:120322000-120322400	Enhancers	Colonic Mucosa	Colon
40	chr1:120322000-120322400	Enhancers	Hela-S3	cervix
41	chr1:120322000-120322600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:120322000-120322600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:120322000-120322600	Enhancers	Duodenum Mucosa	Duodenum
44	chr1:120322000-120322600	Enhancers	Fetal Muscle Leg	muscle
45	chr1:120322000-120322600	Enhancers	Ovary	ovary
46	chr1:120322000-120322800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:120322000-120323000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:120322000-120323000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:120322000-120323000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:120322000-120323600	Flanking Active TSS	Liver	Liver

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