Variant report

Variant	rs12529043
Chromosome Location	chr6:79697855-79697856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11967173	0.87[EUR][1000 genomes]
rs1413967	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415861	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1415862	0.87[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415863	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1538234	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1890230	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28811946	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4547969	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4706748	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706749	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56118785	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58047896	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6454094	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6454095	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6900076	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6906655	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6916942	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6918296	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6923327	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6929315	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6940635	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6941107	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73764080	0.87[EUR][1000 genomes]
rs73764089	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7739298	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7747479	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754715	0.81[EUR][1000 genomes]
rs7756903	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7758407	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7775074	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7776322	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9343862	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9361485	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][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	nsv1015352	chr6:79521820-79757024	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv830705	chr6:79659297-79829530	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv604051	chr6:79691175-79728328	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12529043	GIMAP4	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79648800-79714400	Weak transcription	Gastric	stomach
2	chr6:79649000-79715200	Weak transcription	Stomach Mucosa	stomach
3	chr6:79659200-79702800	Weak transcription	Psoas Muscle	Psoas
4	chr6:79659400-79702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:79659400-79707000	Weak transcription	Esophagus	oesophagus
6	chr6:79659600-79704000	Weak transcription	Lung	lung
7	chr6:79659600-79707000	Weak transcription	Spleen	Spleen
8	chr6:79659800-79702600	Weak transcription	Right Ventricle	heart
9	chr6:79659800-79703400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:79659800-79704000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:79659800-79707000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:79664200-79698000	Weak transcription	Fetal Intestine Small	intestine
13	chr6:79664200-79702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:79669800-79707000	Weak transcription	Aorta	Aorta
15	chr6:79672800-79702600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:79675200-79702200	Weak transcription	Brain Angular Gyrus	brain
17	chr6:79675200-79704600	Weak transcription	Small Intestine	intestine
18	chr6:79675800-79706800	Weak transcription	NHEK	skin
19	chr6:79676000-79703600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:79679200-79698800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:79679800-79702600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:79680000-79702200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:79687000-79698800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:79687000-79709400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:79687000-79714400	Strong transcription	Liver	Liver
26	chr6:79687000-79715800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:79687000-79715800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:79687000-79736000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:79687000-79736200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:79687200-79698000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:79687200-79698200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:79687200-79698600	Strong transcription	HepG2	liver
33	chr6:79687200-79699200	Strong transcription	Placenta	Placenta
34	chr6:79687200-79701000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:79687200-79701000	Strong transcription	Adipose Nuclei	Adipose
36	chr6:79687200-79701200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:79687200-79702800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:79687200-79702800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr6:79687200-79703000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:79687200-79703400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:79687200-79703400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:79687200-79709400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:79687200-79709400	Strong transcription	Fetal Intestine Large	intestine
44	chr6:79687200-79714400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:79687200-79714600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr6:79687200-79714600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr6:79687200-79714800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:79687200-79715000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:79687200-79715400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:79687200-79715600	Strong transcription	Primary B cells from cord blood	blood

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