Variant report

Variant	rs62255994
Chromosome Location	chr3:53279749-53279750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53279512-53279756	HepG2	liver:	n/a	n/a
2	SETDB1	chr3:53279561-53280075	U2OS	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53278235..53282176-chr3:53286915..53291118,4	K562	blood:
2	chr3:53272323..53274896-chr3:53279017..53281047,2	MCF-7	breast:
3	chr3:53266350..53272175-chr3:53273806..53279972,8	K562	blood:
4	chr3:53278223..53280380-chr3:53288212..53291430,4	MCF-7	breast:
5	chr3:53274768..53276711-chr3:53277968..53280467,3	K562	blood:
6	chr3:53274768..53276711-chr3:53278168..53280467,2	K562	blood:
7	chr3:53276936..53279877-chr3:53288649..53290912,2	MCF-7	breast:

No data

Variant related genes	Relation type
TKT	TF binding region
ENSG00000163931	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10433617	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433618	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108506	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030934	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17234771	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235667	0.85[AMR][1000 genomes]
rs41275543	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56654807	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59145995	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255993	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255999	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256000	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256003	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256009	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256043	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256049	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256050	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62256053	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62256965	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256966	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256968	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62256969	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62257004	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62257007	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62257009	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62257011	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62257013	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62257024	0.85[AMR][1000 genomes]
rs73080266	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73082274	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7622159	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830594	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830895	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846315	0.87[EUR][1000 genomes]
rs9850440	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864057	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53257400-53280200	Strong transcription	Dnd41	blood
2	chr3:53269600-53280400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:53270000-53280000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:53272400-53282200	Genic enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:53272600-53280600	Transcr. at gene 5' and 3'	A549	lung
6	chr3:53272800-53286600	Weak transcription	Fetal Brain Male	brain
7	chr3:53272800-53288000	Weak transcription	Fetal Kidney	kidney
8	chr3:53274400-53283600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:53275000-53281600	Weak transcription	K562	blood
10	chr3:53275400-53283200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:53276000-53283400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:53276200-53283800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:53276200-53287400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:53276400-53283400	Weak transcription	Liver	Liver
15	chr3:53276400-53283600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:53276400-53283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:53276400-53283600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:53276400-53284000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:53276600-53279800	Weak transcription	Fetal Brain Female	brain
20	chr3:53276600-53281400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:53276600-53281600	Weak transcription	Thymus	Thymus
22	chr3:53276600-53285200	Weak transcription	HSMM	muscle
23	chr3:53277200-53281800	Weak transcription	GM12878-XiMat	blood
24	chr3:53277200-53285600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:53277600-53281800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:53277600-53286200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:53277800-53282000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:53277800-53284800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:53278000-53281800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:53278000-53282200	Weak transcription	Colonic Mucosa	Colon
31	chr3:53278200-53280000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:53278200-53281800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:53278200-53281800	Weak transcription	Brain Anterior Caudate	brain
34	chr3:53278400-53279800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:53278400-53284200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:53278400-53284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:53278600-53280000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:53278600-53280200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:53278600-53280600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:53278600-53281600	Weak transcription	HUVEC	blood vessel
41	chr3:53278600-53282200	Weak transcription	Primary B cells from cord blood	blood
42	chr3:53278600-53283600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:53278600-53283800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:53278600-53284800	Weak transcription	NH-A	brain
45	chr3:53278600-53285400	Weak transcription	Ovary	ovary
46	chr3:53278600-53285600	Weak transcription	Aorta	Aorta
47	chr3:53278600-53288000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:53278800-53279800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:53278800-53279800	Weak transcription	NHDF-Ad	bronchial
50	chr3:53278800-53280000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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