Variant report

Variant	rs856046
Chromosome Location	chr1:158987941-158987942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1057024	0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs10908699	0.88[ASN][1000 genomes]
rs1101988	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1101997	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1101998	0.97[TSI][hapmap]
rs11265131	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs12059564	0.84[ASN][1000 genomes]
rs1894043	0.92[AFR][1000 genomes]
rs2518563	0.92[AFR][1000 genomes]
rs2518564	0.92[AFR][1000 genomes]
rs2814778	0.82[ASW][hapmap]
rs7535856	0.81[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs856043	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs856044	0.86[ASN][1000 genomes]
rs856049	0.82[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs856050	0.86[EUR][1000 genomes]
rs856054	0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs856066	0.88[ASN][1000 genomes]
rs856068	0.90[ASN][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	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs856046	IFI16	cis	cerebellum	SCAN
rs856046	IFI16	cis	parietal	SCAN
rs856046	TMEM79	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
5	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
6	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
8	chr1:158983600-158988000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:158984000-158988000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung
11	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
12	chr1:158984200-158991400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:158984400-158995200	Strong transcription	Fetal Intestine Large	intestine
15	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
16	chr1:158985400-158988000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:158985400-158988600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:158985400-158988600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:158985400-158988800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:158985400-158989000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:158985600-158988200	Genic enhancers	Left Ventricle	heart
23	chr1:158985600-158988800	Strong transcription	Ovary	ovary
24	chr1:158985600-158991000	Strong transcription	Placenta	Placenta
25	chr1:158985600-158995200	Strong transcription	Thymus	Thymus
26	chr1:158985800-158988000	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr1:158985800-158988800	Strong transcription	NH-A	brain
28	chr1:158985800-158989000	Genic enhancers	Primary T cells from cord blood	blood
29	chr1:158985800-158989000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:158985800-158989200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:158985800-158989600	Weak transcription	Brain Anterior Caudate	brain
32	chr1:158985800-158989800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:158985800-158991000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:158985800-158991600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:158985800-158991600	Strong transcription	Liver	Liver
36	chr1:158985800-158991600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:158985800-158994400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:158985800-158995200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:158985800-159005000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:158986000-158988000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:158986000-158988400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:158986000-158988400	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr1:158986000-158990400	Strong transcription	HMEC	breast
44	chr1:158986000-158990800	Strong transcription	NHEK	skin
45	chr1:158986000-158991200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:158986000-158991600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:158986000-158991600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:158986000-158991800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:158986000-158992400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:158986000-158994000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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