Variant report

Variant	rs56362514
Chromosome Location	chr4:57308990-57308991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
2	chr4:57253395..57255895-chr4:57308484..57311202,2	MCF-7	breast:
3	chr4:57307553..57309303-chr4:57332770..57335058,2	K562	blood:
4	chr4:57306221..57310097-chr4:57330857..57334001,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000270109	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1140982	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1142851	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934479	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934636	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11940993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640212	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12643989	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12643996	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12644498	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649799	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12650288	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1579019	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086759	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086773	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086801	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086804	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17086830	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086838	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086868	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086898	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086909	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086919	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086922	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271924	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34398021	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34419325	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733326	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796539	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796540	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796549	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796550	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4076103	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55778537	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55890437	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55903333	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55909588	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56129706	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56296497	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57245446	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58654038	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59062367	0.80[ASN][1000 genomes]
rs59153415	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59686671	0.84[EUR][1000 genomes]
rs59764923	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59828502	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6830145	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831869	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7437839	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7658340	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7688482	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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
rs56362514	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303000-57309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
3	chr4:57303800-57326000	Weak transcription	Gastric	stomach
4	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
5	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
6	chr4:57304000-57312000	Weak transcription	Left Ventricle	heart
7	chr4:57304000-57315800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
9	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
10	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
11	chr4:57304200-57314600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:57304200-57314800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
14	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:57304400-57310400	Weak transcription	NHLF	lung
18	chr4:57304400-57312600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:57304400-57314000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:57304400-57314000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:57304400-57314600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:57304400-57314600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:57304400-57314600	Weak transcription	Fetal Brain Female	brain
24	chr4:57304400-57314600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:57304400-57314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:57304400-57314800	Weak transcription	Adipose Nuclei	Adipose
27	chr4:57304400-57314800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:57304400-57315200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:57304400-57315600	Weak transcription	Fetal Stomach	stomach
30	chr4:57304400-57317200	Weak transcription	Ovary	ovary
31	chr4:57304400-57317800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:57304400-57318400	Weak transcription	Psoas Muscle	Psoas
33	chr4:57304400-57318600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:57304400-57319800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:57304400-57320200	Weak transcription	Fetal Heart	heart
36	chr4:57304400-57320200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:57304400-57321200	Weak transcription	HSMMtube	muscle
38	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
40	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr4:57305200-57311800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
43	chr4:57306200-57312200	Genic enhancers	HepG2	liver
44	chr4:57306200-57314000	Weak transcription	Fetal Intestine Small	intestine
45	chr4:57306200-57314600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
47	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:57306400-57309000	Strong transcription	Fetal Muscle Leg	muscle
49	chr4:57306400-57312800	Strong transcription	Primary B cells from cord blood	blood
50	chr4:57306600-57310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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