Variant report

Variant	rs17514013
Chromosome Location	chr2:99286794-99286795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10165386	0.83[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10199926	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10207287	0.81[EUR][1000 genomes]
rs1028144	0.86[ASW][hapmap]
rs12467276	0.81[MEX][hapmap];0.83[MKK][hapmap]
rs12468086	0.81[MEX][hapmap];0.81[MKK][hapmap]
rs17448085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448190	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17448211	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17448420	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755756	1.00[CHD][hapmap]
rs2309434	0.84[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3754870	0.86[ASW][hapmap]
rs3769688	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769689	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55633363	0.83[EUR][1000 genomes]
rs55634708	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55646762	0.82[EUR][1000 genomes]
rs55730719	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55859362	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55939630	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56027617	0.83[EUR][1000 genomes]
rs56070038	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163086	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56305624	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56354279	0.82[EUR][1000 genomes]
rs56371690	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56375699	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56945529	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60889948	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62157995	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157997	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62157999	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158000	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158001	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158002	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158008	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62158009	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62158010	0.83[EUR][1000 genomes]
rs62158012	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62158015	0.82[EUR][1000 genomes]
rs6742636	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72825754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs882164	0.81[MEX][hapmap];0.83[MKK][hapmap]

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
rs17514013	MGAT4A	cis	multi-tissue	Pritchard

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
2	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
3	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
4	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
5	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
6	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
9	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:99260000-99288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:99260600-99290400	Weak transcription	Liver	Liver
12	chr2:99260600-99290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:99264600-99299000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:99265200-99291800	Weak transcription	Placenta	Placenta
15	chr2:99265400-99290800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:99265600-99306600	Weak transcription	Lung	lung
17	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
18	chr2:99266200-99290400	Weak transcription	Adipose Nuclei	Adipose
19	chr2:99266200-99296200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:99270600-99293800	Strong transcription	HepG2	liver
22	chr2:99271800-99288800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:99271800-99289400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:99272200-99289000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:99273600-99294600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:99276000-99301400	Weak transcription	Aorta	Aorta
27	chr2:99277600-99291000	Weak transcription	Brain Anterior Caudate	brain
28	chr2:99277600-99291200	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:99277800-99287400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:99278000-99296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:99278200-99290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr2:99279200-99302200	Weak transcription	Right Ventricle	heart
33	chr2:99280600-99292200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:99281400-99295600	Strong transcription	Dnd41	blood
35	chr2:99281800-99292600	Strong transcription	Fetal Intestine Large	intestine
36	chr2:99282400-99290800	Weak transcription	Primary B cells from cord blood	blood
37	chr2:99282800-99306600	Weak transcription	Left Ventricle	heart
38	chr2:99283200-99295000	Strong transcription	Primary T cells from cord blood	blood
39	chr2:99283400-99286800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:99283400-99289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:99283800-99286800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:99283800-99287400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:99284800-99290400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr2:99285200-99295600	Strong transcription	Fetal Thymus	thymus
45	chr2:99285200-99296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:99285600-99287200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:99285800-99295600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:99286000-99287400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:99286000-99291800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:99286200-99286800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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