Variant report

Variant	rs866484
Chromosome Location	chr1:158986477-158986478
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1101991	0.84[JPT][hapmap]
rs1101993	0.88[JPT][hapmap]
rs1101995	0.86[JPT][hapmap]
rs1101996	0.87[JPT][hapmap]
rs1101998	0.84[JPT][hapmap]
rs11265131	0.88[JPT][hapmap]
rs11265133	0.84[JPT][hapmap]
rs12093523	0.88[JPT][hapmap]
rs12094741	0.84[JPT][hapmap]
rs12727764	0.86[TSI][hapmap]
rs2106095	0.84[JPT][hapmap]
rs2276404	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs73021847	0.92[ASN][1000 genomes]
rs7535856	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs856042	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856066	0.93[EUR][1000 genomes]
rs856067	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856068	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs866484	TMEM79	cis	parietal	SCAN
rs866484	IFI16	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	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
9	chr1:158983000-158987200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:158983400-158987200	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr1:158983600-158987200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr1:158983600-158988000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:158984000-158986600	Genic enhancers	HSMMtube	muscle
14	chr1:158984000-158988000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:158984000-158991600	Strong transcription	Fetal Lung	lung
16	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
17	chr1:158984200-158987200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:158984200-158991400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:158984400-158986600	Genic enhancers	Fetal Thymus	thymus
21	chr1:158984400-158987200	Genic enhancers	Hela-S3	cervix
22	chr1:158984400-158995200	Strong transcription	Fetal Intestine Large	intestine
23	chr1:158984600-158987200	Genic enhancers	Spleen	Spleen
24	chr1:158984800-158986800	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
26	chr1:158985400-158986800	Strong transcription	Colonic Mucosa	Colon
27	chr1:158985400-158987200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:158985400-158987200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:158985400-158987200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr1:158985400-158987200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:158985400-158987800	Strong transcription	Fetal Intestine Small	intestine
32	chr1:158985400-158987800	Strong transcription	Fetal Stomach	stomach
33	chr1:158985400-158988000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:158985400-158988600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr1:158985400-158988600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:158985400-158988800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:158985400-158989000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:158985600-158987000	Strong transcription	Brain Substantia Nigra	brain
40	chr1:158985600-158987200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:158985600-158988200	Genic enhancers	Left Ventricle	heart
42	chr1:158985600-158988800	Strong transcription	Ovary	ovary
43	chr1:158985600-158991000	Strong transcription	Placenta	Placenta
44	chr1:158985600-158995200	Strong transcription	Thymus	Thymus
45	chr1:158985800-158986600	Weak transcription	Small Intestine	intestine
46	chr1:158985800-158986800	Genic enhancers	NHDF-Ad	bronchial
47	chr1:158985800-158987000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:158985800-158987000	Genic enhancers	HUVEC	blood vessel
49	chr1:158985800-158987200	Genic enhancers	Primary hematopoietic stem cells	blood
50	chr1:158985800-158987200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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