Variant report

Variant	rs56797870
Chromosome Location	chr3:42672982-42672983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42672452-42673494	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:42672892-42673245	K562	blood:	n/a	n/a
3	POLR2A	chr3:42671968-42673456	K562	blood:	n/a	n/a

Variant related genes	Relation type
NKTR	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085695	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089845	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090902	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095447	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074662	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17074664	0.89[ASN][1000 genomes]
rs17074669	0.89[ASN][1000 genomes]
rs17074673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074680	0.89[ASN][1000 genomes]
rs17074693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284303	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284304	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300057	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300058	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302352	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33969824	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs33984028	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34683820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34687113	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34762478	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34801786	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34852409	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34977988	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35770315	0.89[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36033201	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774402	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774404	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846058	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3846059	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856737	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3886782	0.82[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs57259216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59914338	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60232916	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60348477	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441928	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66786953	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67059259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.81[ASN][1000 genomes]
rs6778982	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795296	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68071013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72864072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7617736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42643600-42675000	Weak transcription	Aorta	Aorta
2	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr3:42647600-42677600	Weak transcription	Gastric	stomach
4	chr3:42650600-42673000	Weak transcription	Esophagus	oesophagus
5	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:42655000-42677800	Weak transcription	Small Intestine	intestine
8	chr3:42655400-42674400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr3:42656600-42673000	Strong transcription	Hela-S3	cervix
11	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:42658200-42673000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:42658200-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:42658400-42691400	Strong transcription	Dnd41	blood
16	chr3:42658600-42677600	Weak transcription	Psoas Muscle	Psoas
17	chr3:42658600-42678400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:42659000-42673000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:42659000-42688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:42660000-42673000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:42660000-42679000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:42661600-42674400	Weak transcription	Fetal Heart	heart
23	chr3:42665000-42679400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:42667200-42674400	Weak transcription	Stomach Mucosa	stomach
25	chr3:42668000-42677000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:42668000-42688200	Strong transcription	Fetal Thymus	thymus
27	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:42668600-42678200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:42668800-42679800	Strong transcription	Osteobl	bone
30	chr3:42668800-42689200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:42668800-42690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:42669000-42690600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
34	chr3:42669200-42692200	Strong transcription	Liver	Liver
35	chr3:42669400-42690600	Strong transcription	K562	blood
36	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:42669600-42676200	Strong transcription	Primary T cells from cord blood	blood
39	chr3:42669600-42690000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:42669800-42676000	Strong transcription	A549	lung
42	chr3:42669800-42679600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:42669800-42680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:42670000-42677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:42670200-42673000	Strong transcription	GM12878-XiMat	blood
46	chr3:42670200-42678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:42670600-42673000	Weak transcription	Fetal Intestine Small	intestine
48	chr3:42670800-42674200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:42671000-42673200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
50	chr3:42671000-42673200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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