Variant report

Variant	rs12040914
Chromosome Location	chr1:246906441-246906442
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	chr1:246892991..246894648-chr1:246905649..246907819,2	MCF-7	breast:
2	chr1:246897168..246899913-chr1:246904406..246907114,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10732299	1.00[AMR][1000 genomes]
rs10924822	1.00[AMR][1000 genomes]
rs12069175	1.00[AMR][1000 genomes]
rs12071299	1.00[AMR][1000 genomes]
rs1691257	1.00[AMR][1000 genomes]
rs1779973	1.00[AMR][1000 genomes]
rs1779976	1.00[AMR][1000 genomes]
rs2996552	1.00[AMR][1000 genomes]
rs3007320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007325	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3007327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3122533	1.00[AMR][1000 genomes]
rs4244625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244626	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244629	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244631	0.87[AFR][1000 genomes]
rs4511163	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4532864	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926452	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926463	1.00[AMR][1000 genomes]
rs6426335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6663093	1.00[AMR][1000 genomes]
rs6696798	1.00[AMR][1000 genomes]
rs7416659	1.00[AMR][1000 genomes]
rs923972	1.00[AMR][1000 genomes]
rs9426266	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9426274	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246889600-246907000	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:246890200-246906600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:246890400-246907400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr1:246890400-246909000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:246890600-246907600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:246891800-246911600	Strong transcription	Liver	Liver
12	chr1:246892400-246912000	Strong transcription	Dnd41	blood
13	chr1:246892600-246908800	Strong transcription	Fetal Stomach	stomach
14	chr1:246892600-246909200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:246893400-246906800	Strong transcription	Brain Cingulate Gyrus	brain
17	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:246894400-246909600	Strong transcription	Placenta	Placenta
19	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
20	chr1:246895000-246906600	Strong transcription	Fetal Intestine Large	intestine
21	chr1:246895000-246907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:246895000-246909000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:246895000-246909200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:246895000-246912000	Weak transcription	Spleen	Spleen
25	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
27	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:246897400-246909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:246897400-246909200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:246897600-246909200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:246897800-246907400	Strong transcription	Adipose Nuclei	Adipose
33	chr1:246899400-246906600	Strong transcription	Ovary	ovary
34	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:246900400-246910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:246900600-246907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:246900600-246908200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:246900800-246908400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:246900800-246912200	Weak transcription	Esophagus	oesophagus
40	chr1:246901000-246908000	Weak transcription	Right Ventricle	heart
41	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:246901800-246908600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:246902000-246909000	Strong transcription	HSMMtube	muscle
44	chr1:246902200-246906600	Strong transcription	HSMM	muscle
45	chr1:246902200-246909000	Strong transcription	NHDF-Ad	bronchial
46	chr1:246902400-246908000	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:246902400-246909000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:246902600-246906800	Weak transcription	Fetal Kidney	kidney
49	chr1:246902600-246912200	Weak transcription	Lung	lung
50	chr1:246902800-246908200	Weak transcription	NHLF	lung

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