Variant report

Variant	rs2913855
Chromosome Location	chr5:177664093-177664094
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr5:177663564-177664138	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr5:177663606-177664126	K562	blood:	n/a	n/a
3	MAX	chr5:177663560-177664143	MCF-7	breast:	n/a	n/a
4	ZNF384	chr5:177663875-177664116	GM12878	blood:	n/a	n/a
5	USF1	chr5:177663659-177664111	K562	blood:	n/a	n/a
6	POLR2A	chr5:177663268-177665103	HL-60	blood:	n/a	n/a
7	POLR2A	chr5:177663195-177665265	HL-60	blood:	n/a	n/a
8	E2F6	chr5:177664012-177664122	K562	blood:	n/a	n/a
9	USF1	chr5:177663664-177664116	K562	blood:	n/a	n/a
10	USF1	chr5:177663652-177664126	HCT-116	colon:	n/a	n/a
11	MAX	chr5:177663564-177664244	MCF-7	breast:	n/a	n/a
12	POLR2A	chr5:177663810-177664133	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177663359..177666352-chr5:177692543..177695366,2	K562	blood:
2	chr5:177663150..177665160-chr5:178157825..178159335,2	MCF-7	breast:
3	chr5:177663620..177664167-chr5:177676965..177677513,2	MCF-7	breast:
4	chr5:177662961..177665111-chr5:178052520..178054523,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHYKPL	TF binding region
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1544926	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549612	0.87[AMR][1000 genomes]
rs2033200	0.86[AMR][1000 genomes]
rs2033201	0.82[AMR][1000 genomes]
rs2913857	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2913858	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2913859	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2913860	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2973807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890811	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1018031	chr5:177655010-177746378	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv537969	chr5:177655010-177746378	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv883195	chr5:177655194-177690539	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv883196	chr5:177655194-177690978	Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv883197	chr5:177655194-177707204	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv1025291	chr5:177657927-177756215	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv537970	chr5:177657927-177756215	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv527792	chr5:177659075-177675217	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv883198	chr5:177659075-177690539	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv883199	chr5:177661902-177717640	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2913855	AGXT2L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177659800-177665800	Weak transcription	Gastric	stomach
2	chr5:177660000-177664600	Weak transcription	Small Intestine	intestine
3	chr5:177660200-177664600	Weak transcription	HSMM	muscle
4	chr5:177660200-177665200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:177660200-177665800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr5:177660200-177667000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr5:177660200-177667000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:177660200-177667600	Enhancers	Fetal Muscle Trunk	muscle
9	chr5:177660400-177664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:177660400-177664200	Weak transcription	Esophagus	oesophagus
11	chr5:177660400-177664200	Weak transcription	HSMMtube	muscle
12	chr5:177660400-177664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:177660400-177664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:177660400-177665800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:177660400-177665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:177660400-177666200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:177660400-177668000	Enhancers	Primary hematopoietic stem cells	blood
18	chr5:177660600-177664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:177660600-177664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:177661200-177664400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr5:177661200-177666400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr5:177661400-177666200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:177661400-177667800	Enhancers	Adipose Nuclei	Adipose
24	chr5:177661400-177669600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr5:177661600-177666400	Enhancers	Fetal Muscle Leg	muscle
26	chr5:177661600-177671600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:177661800-177665400	Enhancers	Spleen	Spleen
28	chr5:177661800-177666400	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:177661800-177666600	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr5:177661800-177667600	Enhancers	Liver	Liver
31	chr5:177661800-177669800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr5:177662000-177665600	Enhancers	Pancreas	Pancrea
33	chr5:177662200-177664200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:177662200-177665000	Weak transcription	Primary B cells from cord blood	blood
35	chr5:177662200-177665400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:177662200-177665400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:177662200-177665600	Weak transcription	Primary T cells from cord blood	blood
38	chr5:177662200-177674800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:177662600-177665000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:177662600-177665800	Weak transcription	Thymus	Thymus
41	chr5:177662600-177667600	Weak transcription	Dnd41	blood
42	chr5:177662600-177669600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:177663000-177664200	Weak transcription	Lung	lung
44	chr5:177663000-177665600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr5:177663200-177664800	Enhancers	K562	blood
46	chr5:177663200-177665000	Enhancers	NHDF-Ad	bronchial
47	chr5:177663200-177665600	Enhancers	Stomach Mucosa	stomach
48	chr5:177663200-177667600	Enhancers	Left Ventricle	heart
49	chr5:177663400-177664200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:177663400-177664400	Enhancers	Duodenum Smooth Muscle	Duodenum

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