Variant report

Variant	rs56672277
Chromosome Location	chr4:57227375-57227376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10010544	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11133443	0.90[ASN][1000 genomes]
rs12645138	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271925	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34510373	0.90[ASN][1000 genomes]
rs3796548	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3822001	0.91[ASN][1000 genomes]
rs4565139	0.89[ASN][1000 genomes]
rs55959996	0.94[EUR][1000 genomes]
rs56066795	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56356367	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59997251	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60104031	0.91[ASN][1000 genomes]
rs67343558	0.90[ASN][1000 genomes]
rs67721941	0.86[ASN][1000 genomes]
rs6836118	0.84[ASN][1000 genomes]
rs6853418	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73167398	0.86[ASN][1000 genomes]
rs7693372	0.86[ASN][1000 genomes]
rs7696808	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56672277	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
3	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
5	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
6	chr4:57203200-57235200	Weak transcription	Osteobl	bone
7	chr4:57203200-57251800	Weak transcription	A549	lung
8	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:57204000-57252200	Weak transcription	NH-A	brain
11	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
14	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:57205200-57228200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:57205200-57229200	Weak transcription	Brain Germinal Matrix	brain
17	chr4:57205400-57228000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
21	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
23	chr4:57213200-57229200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:57213400-57252200	Weak transcription	NHLF	lung
26	chr4:57213600-57250200	Weak transcription	K562	blood
27	chr4:57213600-57252000	Weak transcription	HMEC	breast
28	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:57214800-57227800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr4:57214800-57229000	Weak transcription	Fetal Thymus	thymus
32	chr4:57215000-57238000	Weak transcription	Brain Substantia Nigra	brain
33	chr4:57215800-57228400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
35	chr4:57216000-57228800	Weak transcription	Dnd41	blood
36	chr4:57216000-57235800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:57216000-57236400	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:57216000-57241200	Weak transcription	Pancreas	Pancrea
39	chr4:57216000-57251800	Weak transcription	HepG2	liver
40	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:57216200-57245600	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:57216200-57246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:57216400-57228600	Weak transcription	GM12878-XiMat	blood
46	chr4:57216400-57229200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
48	chr4:57218400-57239000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr4:57218400-57241200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:57219000-57235200	Weak transcription	Primary B cells from peripheral blood	blood

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