Variant report

Variant	rs56003368
Chromosome Location	chr4:84504777-84504778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:84498347..84499871-chr4:84502515..84505329,2	K562	blood:
2	chr4:84503642..84506316-chr4:84508887..84511380,3	K562	blood:
3	chr4:84503632..84505434-chr4:84510296..84512345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138678	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10002139	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10012782	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11099607	0.81[ASN][1000 genomes]
rs1123378	0.81[ASN][1000 genomes]
rs11721920	0.83[ASN][1000 genomes]
rs11722160	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11723311	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730975	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11731267	0.81[ASN][1000 genomes]
rs11731336	0.81[ASN][1000 genomes]
rs11733281	0.83[ASN][1000 genomes]
rs11733610	0.81[ASN][1000 genomes]
rs11734158	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11736724	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11737424	0.83[ASN][1000 genomes]
rs12331130	0.83[ASN][1000 genomes]
rs12331142	0.83[ASN][1000 genomes]
rs12331198	0.83[ASN][1000 genomes]
rs12331205	0.83[ASN][1000 genomes]
rs12331922	0.83[ASN][1000 genomes]
rs1521532	0.81[ASN][1000 genomes]
rs17006888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17353060	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17355300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17355321	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17355349	0.81[ASN][1000 genomes]
rs17355391	0.81[ASN][1000 genomes]
rs1965464	0.82[ASN][1000 genomes]
rs28463240	0.83[ASN][1000 genomes]
rs28482178	0.83[ASN][1000 genomes]
rs28504032	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28542730	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28587748	0.83[ASN][1000 genomes]
rs28615868	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28710332	0.83[ASN][1000 genomes]
rs35434386	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733327	0.82[ASN][1000 genomes]
rs3733329	0.82[ASN][1000 genomes]
rs4693092	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4693093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693633	0.81[ASN][1000 genomes]
rs55724846	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55839835	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55851819	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56191639	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56208893	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56394927	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62303966	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303968	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303974	0.81[ASN][1000 genomes]
rs62303975	0.81[ASN][1000 genomes]
rs62305330	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305331	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305332	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305333	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305334	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305335	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62305336	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62305339	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62305340	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62305342	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62305343	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6812240	0.83[ASN][1000 genomes]
rs6812267	0.83[ASN][1000 genomes]
rs6835060	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6835481	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72654969	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72654977	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72654978	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72654987	0.81[ASN][1000 genomes]
rs9307826	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829994	chr4:84366299-84558316	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv879512	chr4:84374692-85090749	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1010009	chr4:84469896-84882528	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56003368	MAG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:84486000-84513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:84488600-84516800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:84492000-84512200	Weak transcription	NHEK	skin
4	chr4:84495600-84516600	Weak transcription	Fetal Intestine Large	intestine
5	chr4:84495600-84516800	Weak transcription	Right Ventricle	heart
6	chr4:84500000-84512800	Weak transcription	Fetal Intestine Small	intestine
7	chr4:84503400-84506000	Enhancers	Fetal Lung	lung
8	chr4:84503600-84520400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:84503600-84525800	Weak transcription	Psoas Muscle	Psoas
10	chr4:84503800-84506800	Weak transcription	Left Ventricle	heart
11	chr4:84503800-84508800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:84503800-84508800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:84503800-84510400	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:84503800-84512200	Weak transcription	Adipose Nuclei	Adipose
15	chr4:84503800-84512200	Weak transcription	Right Atrium	heart
16	chr4:84503800-84516600	Weak transcription	NH-A	brain
17	chr4:84503800-84516800	Weak transcription	Spleen	Spleen
18	chr4:84503800-84524000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:84503800-84524400	Weak transcription	Lung	lung
20	chr4:84503800-84525800	Weak transcription	Colonic Mucosa	Colon
21	chr4:84503800-84527200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:84503800-84528200	Weak transcription	Gastric	stomach
23	chr4:84504000-84509000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:84504000-84509800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:84504000-84514600	Weak transcription	Fetal Brain Male	brain
26	chr4:84504000-84520200	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:84504000-84524000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:84504200-84505200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:84504200-84505200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:84504200-84505200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:84504200-84507400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:84504200-84509000	Weak transcription	A549	lung
33	chr4:84504200-84509800	Weak transcription	Small Intestine	intestine
34	chr4:84504200-84510400	Weak transcription	HMEC	breast
35	chr4:84504200-84512200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:84504200-84516000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:84504200-84516600	Weak transcription	Ovary	ovary
38	chr4:84504200-84520400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:84504200-84520400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:84504200-84524000	Weak transcription	Fetal Heart	heart
41	chr4:84504200-84524000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:84504200-84524000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:84504400-84505000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:84504400-84505600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr4:84504400-84507200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr4:84504400-84526600	Weak transcription	Rectal Mucosa Donor 29	rectum

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