Variant report

Variant	rs7296090
Chromosome Location	chr12:106900305-106900306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10444532	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10778465	0.82[EUR][1000 genomes]
rs10778469	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10778473	0.81[EUR][1000 genomes]
rs10778474	0.81[EUR][1000 genomes]
rs10778476	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778485	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861577	0.95[CEU][hapmap]
rs10861578	0.95[CEU][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10861581	0.90[CEU][hapmap]
rs10861585	0.85[CEU][hapmap]
rs10861592	0.90[CEU][hapmap];0.85[MEX][hapmap]
rs10861593	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10861595	0.82[EUR][1000 genomes]
rs10861601	0.95[CEU][hapmap]
rs10861605	0.85[AMR][1000 genomes]
rs10861608	0.88[EUR][1000 genomes]
rs10861614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112953	0.95[CEU][hapmap]
rs11112961	0.82[EUR][1000 genomes]
rs11112992	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11113004	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11113009	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11113011	0.97[ASN][1000 genomes]
rs11113024	0.97[ASN][1000 genomes]
rs11609315	0.84[EUR][1000 genomes]
rs11611176	0.84[EUR][1000 genomes]
rs12423068	0.88[EUR][1000 genomes]
rs12425459	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17038414	0.82[EUR][1000 genomes]
rs17221107	0.86[ASN][1000 genomes]
rs17285274	0.95[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2288268	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374610	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28475238	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2900499	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2900500	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3851631	0.84[EUR][1000 genomes]
rs4522273	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625578	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61941918	0.87[EUR][1000 genomes]
rs61941920	0.87[EUR][1000 genomes]
rs61941943	0.85[AMR][1000 genomes]
rs61941944	0.80[EUR][1000 genomes]
rs61943690	0.82[EUR][1000 genomes]
rs67966244	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7307711	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309020	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7296090	CKAP4	cis	cerebellum	SCAN
rs7296090	STAB2	cis	parietal	SCAN
rs7296090	ANO1	trans	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106886200-106916400	Weak transcription	A549	lung
4	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine
5	chr12:106888200-106906800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:106888800-106900400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:106889200-106903200	Weak transcription	HMEC	breast
8	chr12:106889200-106904600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:106889200-106905400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:106889400-106904000	Strong transcription	Primary T cells from cord blood	blood
11	chr12:106889400-106904600	Strong transcription	Liver	Liver
12	chr12:106889800-106901600	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:106890000-106904200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr12:106890400-106901400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:106890800-106905200	Weak transcription	Colonic Mucosa	Colon
16	chr12:106891200-106901600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr12:106892000-106904400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:106892000-106905200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:106892000-106906400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:106892000-106907800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:106892200-106901200	Weak transcription	Fetal Kidney	kidney
22	chr12:106892400-106905200	Weak transcription	NHEK	skin
23	chr12:106892800-106904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:106892800-106905600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:106894400-106916400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:106894600-106905200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:106894600-106913200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:106894800-106900400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:106894800-106901000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:106895600-106900600	Strong transcription	Lung	lung
31	chr12:106895600-106904000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:106896000-106901000	Weak transcription	GM12878-XiMat	blood
33	chr12:106896400-106906600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:106896400-106906800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:106896400-106907200	Weak transcription	Esophagus	oesophagus
36	chr12:106896400-106908400	Weak transcription	NHLF	lung
37	chr12:106896400-106916800	Weak transcription	Fetal Intestine Small	intestine
38	chr12:106896600-106902200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:106896600-106905200	Weak transcription	Fetal Heart	heart
40	chr12:106896600-106906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:106897000-106905000	Weak transcription	Right Atrium	heart
42	chr12:106897400-106900800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:106897400-106905600	Strong transcription	Placenta	Placenta
44	chr12:106897600-106901000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:106897600-106901600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:106897600-106902400	Strong transcription	Left Ventricle	heart
47	chr12:106897800-106901000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:106897800-106901600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:106897800-106904000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:106898200-106903200	Weak transcription	Aorta	Aorta

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