Variant report

Variant	rs6787817
Chromosome Location	chr3:53324569-53324570
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	chr3:53324080-53326867	K562	blood:	n/a	n/a
2	POLR2A	chr3:53324392-53324569	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
DCP1A	TF binding region
ENSG00000206902	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11919567	1.00[AMR][1000 genomes]
rs11920772	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11925433	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030942	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052997	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17053116	1.00[AMR][1000 genomes]
rs58338691	1.00[AMR][1000 genomes]
rs60350276	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61299945	1.00[AMR][1000 genomes]
rs68140464	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954817	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954820	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954825	1.00[AMR][1000 genomes]
rs72954827	1.00[AMR][1000 genomes]
rs72954837	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957594	0.96[AFR][1000 genomes];1.00[AMR][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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53304600-53325600	Weak transcription	Fetal Heart	heart
2	chr3:53304600-53326200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:53309400-53351200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:53309800-53325600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:53309800-53326200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:53312200-53337400	Weak transcription	Psoas Muscle	Psoas
7	chr3:53312400-53328000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:53314200-53325600	Weak transcription	Colonic Mucosa	Colon
9	chr3:53314200-53326400	Weak transcription	K562	blood
10	chr3:53315200-53326800	Strong transcription	Primary B cells from cord blood	blood
11	chr3:53315200-53333800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:53315200-53338400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:53316400-53333600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:53316400-53337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:53316600-53327200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:53316600-53327200	Strong transcription	Liver	Liver
17	chr3:53316600-53329200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:53316600-53333600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:53316600-53333800	Strong transcription	Placenta	Placenta
20	chr3:53316600-53338600	Strong transcription	Fetal Muscle Leg	muscle
21	chr3:53317000-53326000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:53317200-53332600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:53317400-53332200	Weak transcription	Small Intestine	intestine
24	chr3:53317800-53329200	Strong transcription	Fetal Intestine Small	intestine
25	chr3:53317800-53330600	Strong transcription	Fetal Stomach	stomach
26	chr3:53318000-53327400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:53318000-53328800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:53318000-53329200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:53318000-53345000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:53318000-53345800	Weak transcription	Stomach Mucosa	stomach
31	chr3:53318600-53327000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:53318600-53327200	Strong transcription	Fetal Lung	lung
33	chr3:53319400-53326000	Weak transcription	Esophagus	oesophagus
34	chr3:53319400-53326000	Weak transcription	Pancreas	Pancrea
35	chr3:53319800-53326000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:53319800-53326000	Weak transcription	Ovary	ovary
37	chr3:53320000-53325600	Weak transcription	HMEC	breast
38	chr3:53320200-53326800	Strong transcription	Brain Germinal Matrix	brain
39	chr3:53320600-53332400	Weak transcription	Hela-S3	cervix
40	chr3:53321000-53325600	Weak transcription	A549	lung
41	chr3:53321000-53326000	Weak transcription	NHLF	lung
42	chr3:53321200-53327000	Strong transcription	Fetal Thymus	thymus
43	chr3:53321400-53324600	Strong transcription	Spleen	Spleen
44	chr3:53321400-53325000	Weak transcription	HUVEC	blood vessel
45	chr3:53321400-53326000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:53321400-53326000	Weak transcription	Aorta	Aorta
47	chr3:53321600-53326000	Weak transcription	NHDF-Ad	bronchial
48	chr3:53321800-53326000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:53321800-53326600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:53321800-53337400	Weak transcription	Fetal Kidney	kidney

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