Variant report

Variant	rs55859362
Chromosome Location	chr2:99284546-99284547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10165386	0.82[EUR][1000 genomes]
rs10199926	0.85[EUR][1000 genomes]
rs17448085	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17448190	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17448211	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17448420	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17514013	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309434	0.84[EUR][1000 genomes]
rs3769688	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3769689	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55633363	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55634708	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55646762	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55730719	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55939630	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56027617	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56070038	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56163086	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56305624	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56354279	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56371690	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56375699	0.84[EUR][1000 genomes]
rs56945529	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60889948	0.84[EUR][1000 genomes]
rs62157995	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62157997	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62157999	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62158000	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62158001	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62158002	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62158008	0.84[EUR][1000 genomes]
rs62158009	0.84[EUR][1000 genomes]
rs62158010	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62158012	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62158015	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6742636	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72825754	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv582516	chr2:99254031-99304794	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55859362	MGAT4A	cis	intralobular white matter	BrainEAC

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
2	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
3	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
4	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
5	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
6	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
7	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
10	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:99260000-99288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:99260600-99290400	Weak transcription	Liver	Liver
13	chr2:99260600-99290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:99264600-99299000	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:99265200-99291800	Weak transcription	Placenta	Placenta
16	chr2:99265400-99290800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:99265600-99306600	Weak transcription	Lung	lung
18	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:99266200-99290400	Weak transcription	Adipose Nuclei	Adipose
20	chr2:99266200-99296200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:99270600-99293800	Strong transcription	HepG2	liver
23	chr2:99271800-99288800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:99271800-99289400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:99272200-99289000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:99273600-99294600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:99276000-99285800	Weak transcription	Pancreas	Pancrea
28	chr2:99276000-99301400	Weak transcription	Aorta	Aorta
29	chr2:99276200-99284800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:99277600-99291000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:99277600-99291200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:99277800-99287400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:99278000-99296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:99278200-99290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:99279200-99286400	Weak transcription	HUVEC	blood vessel
36	chr2:99279200-99302200	Weak transcription	Right Ventricle	heart
37	chr2:99279400-99284800	Weak transcription	Thymus	Thymus
38	chr2:99280600-99292200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:99281200-99286200	Weak transcription	Gastric	stomach
40	chr2:99281400-99286200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:99281400-99295600	Strong transcription	Dnd41	blood
42	chr2:99281600-99286200	Weak transcription	HMEC	breast
43	chr2:99281800-99292600	Strong transcription	Fetal Intestine Large	intestine
44	chr2:99282400-99290800	Weak transcription	Primary B cells from cord blood	blood
45	chr2:99282800-99284600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:99282800-99284800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:99282800-99286200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:99282800-99286400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:99282800-99306600	Weak transcription	Left Ventricle	heart
50	chr2:99283000-99284800	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links