Variant report

Variant	rs56975801
Chromosome Location	chr1:246907038-246907039
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: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10924816	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10924827	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11581735	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023715	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026095	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12042435	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703972	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3314	0.85[EUR][1000 genomes]
rs41267531	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56338592	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57384976	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58542205	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60107954	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426330	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671220	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414184	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7417422	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:246890400-246907400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr1:246890400-246909000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:246890600-246907600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:246891800-246911600	Strong transcription	Liver	Liver
10	chr1:246892400-246912000	Strong transcription	Dnd41	blood
11	chr1:246892600-246908800	Strong transcription	Fetal Stomach	stomach
12	chr1:246892600-246909200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:246894400-246909600	Strong transcription	Placenta	Placenta
16	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
17	chr1:246895000-246907400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:246895000-246909000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:246895000-246909200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:246895000-246912000	Weak transcription	Spleen	Spleen
21	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
23	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:246897400-246909000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:246897400-246909200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:246897600-246909200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:246897800-246907400	Strong transcription	Adipose Nuclei	Adipose
29	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:246900400-246910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:246900600-246907200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:246900600-246908200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:246900800-246908400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:246900800-246912200	Weak transcription	Esophagus	oesophagus
35	chr1:246901000-246908000	Weak transcription	Right Ventricle	heart
36	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:246901800-246908600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:246902000-246909000	Strong transcription	HSMMtube	muscle
39	chr1:246902200-246909000	Strong transcription	NHDF-Ad	bronchial
40	chr1:246902400-246908000	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:246902400-246909000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:246902600-246912200	Weak transcription	Lung	lung
43	chr1:246902800-246908200	Weak transcription	NHLF	lung
44	chr1:246902800-246908400	Weak transcription	Brain Angular Gyrus	brain
45	chr1:246902800-246908400	Weak transcription	Gastric	stomach
46	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
47	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:246903000-246907800	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:246903000-246909200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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