Variant report

Variant	rs55839835
Chromosome Location	chr4:84495373-84495374
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:84456699..84458274-chr4:84494162..84496351,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138678	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10002139	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10009351	0.81[EUR][1000 genomes]
rs10012782	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11721920	0.93[ASN][1000 genomes]
rs11722160	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11723311	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11730975	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731267	0.90[ASN][1000 genomes]
rs11731336	0.90[ASN][1000 genomes]
rs11733281	0.93[ASN][1000 genomes]
rs11734158	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737424	0.93[ASN][1000 genomes]
rs12331130	0.93[ASN][1000 genomes]
rs12331142	0.93[ASN][1000 genomes]
rs12331198	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12331205	0.93[ASN][1000 genomes]
rs12331922	0.93[ASN][1000 genomes]
rs17006888	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17353060	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355300	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17355321	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965464	0.91[ASN][1000 genomes]
rs28463240	0.93[ASN][1000 genomes]
rs28482178	0.93[ASN][1000 genomes]
rs28504032	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28542730	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28587748	0.93[ASN][1000 genomes]
rs28615868	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28710332	0.93[ASN][1000 genomes]
rs35434386	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693093	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55724846	0.89[EUR][1000 genomes]
rs55851819	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56003368	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56191639	0.87[EUR][1000 genomes]
rs56208893	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56394927	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62303966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62303968	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305330	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305331	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305332	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305333	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305334	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305335	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62305336	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305339	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62305340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305342	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305343	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812240	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812267	0.93[ASN][1000 genomes]
rs6835060	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6835481	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72654969	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72654977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72654978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307826	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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	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
4	nsv964299	chr4:84490085-84499608	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55839835	MAG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:84481200-84503200	Weak transcription	Colon Smooth Muscle	Colon
2	chr4:84482800-84503400	Weak transcription	Ovary	ovary
3	chr4:84486000-84513000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:84488600-84516800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:84489400-84503400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:84489800-84499600	Weak transcription	Fetal Lung	lung
7	chr4:84490800-84502800	Weak transcription	Left Ventricle	heart
8	chr4:84491400-84498000	Weak transcription	Right Atrium	heart
9	chr4:84491600-84502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:84491600-84503200	Weak transcription	HMEC	breast
11	chr4:84492000-84512200	Weak transcription	NHEK	skin
12	chr4:84492200-84502600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:84492600-84499600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:84492600-84499600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:84494000-84495600	Enhancers	Fetal Heart	heart
16	chr4:84494000-84495600	Enhancers	Fetal Intestine Small	intestine
17	chr4:84494000-84495600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:84494400-84495600	Enhancers	Fetal Intestine Large	intestine
19	chr4:84494600-84495400	Enhancers	Duodenum Mucosa	Duodenum
20	chr4:84494600-84495600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr4:84494800-84495400	Enhancers	Small Intestine	intestine
22	chr4:84494800-84495600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:84494800-84502600	Weak transcription	Psoas Muscle	Psoas
24	chr4:84495000-84495600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr4:84495000-84495600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr4:84495200-84495400	Enhancers	Liver	Liver
27	chr4:84495200-84495400	Genic enhancers	A549	lung
28	chr4:84495200-84495600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:84495200-84495600	Enhancers	Adipose Nuclei	Adipose
30	chr4:84495200-84495600	Enhancers	Right Ventricle	heart
31	chr4:84495200-84495800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:84495200-84495800	Enhancers	Fetal Kidney	kidney
33	chr4:84495200-84495800	Enhancers	HepG2	liver

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