Variant report

Variant	rs58318788
Chromosome Location	chr1:161020432-161020433
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161020317-161020733	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160965107..160967123-chr1:161018782..161021042,2	MCF-7	breast:
2	chr1:161019790..161021495-chr1:161129242..161131145,2	MCF-7	breast:
3	chr1:160991163..160993549-chr1:161020053..161022442,2	MCF-7	breast:
4	chr1:161018354..161021283-chr1:161024769..161026655,3	K562	blood:
5	chr1:161019865..161020445-chr1:161067098..161067648,2	K562	blood:
6	chr1:161018427..161020724-chr1:161039039..161040672,2	K562	blood:

No data

Variant related genes	Relation type
USF1	TF binding region
ENSG00000186517	Chromatin interaction
ENSG00000143258	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12036299	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1556259	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1556260	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1974140	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073653	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3766382	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3766383	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs58974723	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427572	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6427573	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6660240	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686076	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7516231	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016200-161022600	Weak transcription	Gastric	stomach
2	chr1:161016400-161020800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:161016400-161022600	Weak transcription	Small Intestine	intestine
4	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
5	chr1:161016600-161022200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:161016600-161024200	Weak transcription	Right Ventricle	heart
7	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:161016800-161021800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:161017000-161022000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:161017000-161024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
13	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:161017200-161021200	Weak transcription	Stomach Mucosa	stomach
16	chr1:161017200-161022000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:161017200-161029200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:161017200-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:161017400-161022600	Weak transcription	K562	blood
20	chr1:161017400-161027400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr1:161017400-161027400	Strong transcription	Dnd41	blood
22	chr1:161017400-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:161017400-161031000	Strong transcription	Thymus	Thymus
24	chr1:161017600-161021000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:161017600-161024000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
27	chr1:161017800-161024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:161017800-161026200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:161018000-161025800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:161018000-161027400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:161018200-161026800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:161018400-161026000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:161018400-161026400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:161018400-161027400	Strong transcription	GM12878-XiMat	blood
35	chr1:161018600-161024200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
37	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:161018800-161022200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:161018800-161028200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:161019000-161021000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:161019000-161026600	Strong transcription	Placenta	Placenta
42	chr1:161019200-161021000	Weak transcription	Pancreas	Pancrea
43	chr1:161019400-161021200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:161019400-161026000	Strong transcription	Spleen	Spleen
45	chr1:161019400-161029400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:161019600-161020800	Weak transcription	Lung	lung
47	chr1:161019600-161021000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:161019600-161021000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:161019600-161021600	Genic enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:161019600-161022600	Weak transcription	Adipose Nuclei	Adipose

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