Variant report

Variant	rs859141
Chromosome Location	chr12:25222024-25222025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1683166	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17387019	0.87[GIH][hapmap]
rs17388148	1.00[GIH][hapmap]
rs7313952	0.89[EUR][1000 genomes]
rs7976264	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7980388	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases
4	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs859141	PDGFD	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25205800-25224800	Weak transcription	Lung	lung
2	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:25212000-25250800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:25214200-25224000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:25214400-25224200	Weak transcription	Stomach Mucosa	stomach
7	chr12:25214400-25245600	Weak transcription	Ovary	ovary
8	chr12:25214400-25251800	Weak transcription	Fetal Intestine Large	intestine
9	chr12:25214800-25223800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:25214800-25225400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:25215000-25223400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:25215000-25226800	Strong transcription	Primary T cells from cord blood	blood
13	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:25215200-25224000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:25215400-25223800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:25215400-25224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:25215400-25225400	Strong transcription	Primary B cells from cord blood	blood
18	chr12:25215400-25228000	Strong transcription	Fetal Thymus	thymus
19	chr12:25215800-25226000	Strong transcription	Dnd41	blood
20	chr12:25216000-25224000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr12:25216000-25227200	Strong transcription	Thymus	Thymus
22	chr12:25216200-25226600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr12:25216400-25223200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:25216600-25222800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:25216600-25223400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:25216600-25223600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:25216600-25224000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:25216800-25222200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:25217000-25223600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:25218400-25223400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:25218600-25239200	Weak transcription	Fetal Intestine Small	intestine
32	chr12:25218800-25222200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:25218800-25227200	Weak transcription	Pancreas	Pancrea
34	chr12:25219400-25225400	Weak transcription	Left Ventricle	heart
35	chr12:25219800-25223800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:25221200-25225200	Genic enhancers	GM12878-XiMat	blood
37	chr12:25221400-25222400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:25221600-25222400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:25221600-25229200	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr12:25221600-25235800	Weak transcription	Liver	Liver
41	chr12:25221800-25222200	Genic enhancers	Adipose Nuclei	Adipose
42	chr12:25221800-25222600	Weak transcription	Spleen	Spleen

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