Variant report

Variant	rs1391129
Chromosome Location	chr12:59992011-59992012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10747849	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783990	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877316	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187991	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2132874	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2365663	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2671853	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2671855	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs402342	0.81[ASW][hapmap]
rs4760290	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][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	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1391129	STAT6	cis	parietal	SCAN
rs1391129	NXPH4	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59990800-59992200	Flanking Active TSS	Fetal Heart	heart
2	chr12:59991000-60005000	Weak transcription	Lung	lung
3	chr12:59991200-60004600	Weak transcription	Ovary	ovary
4	chr12:59991400-59992200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:59991400-59992200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:59991400-59992200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:59991400-59992600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr12:59991400-59992800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:59991400-59992800	Weak transcription	Small Intestine	intestine
10	chr12:59991400-59993400	Weak transcription	Right Ventricle	heart
11	chr12:59991400-59994000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:59991400-59994800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr12:59991400-59994800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:59991400-59995400	Weak transcription	Psoas Muscle	Psoas
15	chr12:59991400-59998800	Weak transcription	Left Ventricle	heart
16	chr12:59991400-60004600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:59991400-60004600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:59991400-60004600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:59991400-60005000	Weak transcription	Pancreas	Pancrea
20	chr12:59991400-60009400	Weak transcription	Gastric	stomach
21	chr12:59991600-59992200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:59991600-59992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:59991600-59992200	Enhancers	Brain Hippocampus Middle	brain
24	chr12:59991600-59992200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:59991600-59992200	Enhancers	Stomach Smooth Muscle	stomach
26	chr12:59991600-59992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:59991600-59992400	Weak transcription	Brain Angular Gyrus	brain
28	chr12:59991600-59992600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:59991600-59992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:59991600-59992800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:59991600-59992800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:59991600-59992800	Weak transcription	HUVEC	blood vessel
33	chr12:59991600-59994400	Enhancers	Adipose Nuclei	Adipose
34	chr12:59991600-59999000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:59991600-60003600	Weak transcription	Fetal Thymus	thymus
36	chr12:59991600-60004400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:59991600-60004600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:59991600-60004600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:59991600-60004600	Weak transcription	Brain Anterior Caudate	brain
40	chr12:59991600-60004800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:59991600-60005000	Weak transcription	Thymus	Thymus
42	chr12:59991600-60009400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:59991800-59992200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:59991800-59992200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:59991800-59992200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:59991800-59992200	Enhancers	Fetal Brain Male	brain
47	chr12:59991800-59992200	Flanking Active TSS	NHDF-Ad	bronchial
48	chr12:59991800-59992400	Enhancers	Hela-S3	cervix
49	chr12:59991800-59992600	Enhancers	Dnd41	blood
50	chr12:59991800-59993400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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