Variant report

Variant	rs494005
Chromosome Location	chr12:118738700-118738701
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1092854	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1151901	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1277175	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs353885	0.85[AMR][1000 genomes]
rs353886	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353887	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353889	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353890	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353892	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353896	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs364823	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs404566	0.92[ASN][1000 genomes]
rs410747	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418941	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs456228	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs465735	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs484838	0.83[ASN][1000 genomes]
rs492939	0.83[ASN][1000 genomes]
rs503548	0.83[ASN][1000 genomes]
rs519480	0.83[ASN][1000 genomes]
rs523011	0.83[ASN][1000 genomes]
rs566437	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs571113	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs575121	0.93[ASN][1000 genomes]
rs708862	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs708863	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793596	0.82[ASN][1000 genomes]
rs795481	0.82[ASN][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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:118677000-118739800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:118683400-118739800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:118694600-118739800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:118704000-118739000	Weak transcription	NHDF-Ad	bronchial
8	chr12:118712200-118739000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:118715000-118741200	Weak transcription	Thymus	Thymus
11	chr12:118719200-118744400	Weak transcription	HSMM	muscle
12	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:118721400-118739800	Weak transcription	Left Ventricle	heart
14	chr12:118721600-118739400	Weak transcription	Psoas Muscle	Psoas
15	chr12:118722600-118739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:118726600-118746800	Weak transcription	Lung	lung
18	chr12:118728200-118739000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:118728400-118744400	Weak transcription	NHLF	lung
20	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
23	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:118735400-118738800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
28	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:118736600-118742600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:118737400-118739800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr12:118737600-118739200	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:118737600-118739800	Weak transcription	Liver	Liver
33	chr12:118737600-118741200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:118737800-118739800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:118738000-118740000	Enhancers	K562	blood
36	chr12:118738000-118740200	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:118738000-118742000	Enhancers	NHEK	skin
38	chr12:118738000-118744600	Weak transcription	Fetal Intestine Small	intestine
39	chr12:118738000-118745000	Weak transcription	Small Intestine	intestine
40	chr12:118738200-118741200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:118738200-118744400	Weak transcription	NH-A	brain
42	chr12:118738200-118745200	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
44	chr12:118738400-118738800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:118738400-118738800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:118738400-118738800	Enhancers	GM12878-XiMat	blood
47	chr12:118738400-118739000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:118738400-118740400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr12:118738400-118741200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:118738400-118744800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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