Variant report

Variant	rs302337
Chromosome Location	chr12:29906149-29906150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10743672	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10743673	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10743674	0.92[AMR][1000 genomes]
rs10771578	0.90[AMR][1000 genomes]
rs10771579	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10771580	0.90[AMR][1000 genomes]
rs10843501	0.86[AMR][1000 genomes]
rs10843502	0.84[AMR][1000 genomes]
rs10843503	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10843504	0.92[AMR][1000 genomes]
rs11609828	0.88[AMR][1000 genomes]
rs12231167	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12810794	0.85[AMR][1000 genomes]
rs1551930	0.84[AMR][1000 genomes]
rs2882467	1.00[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[AMR][1000 genomes]
rs302335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302338	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4244848	0.92[AMR][1000 genomes]
rs4244849	0.92[AMR][1000 genomes]
rs4931215	0.93[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4931216	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4931217	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4931218	0.90[AMR][1000 genomes]
rs4931219	1.00[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4931220	0.92[AMR][1000 genomes]
rs7967779	0.81[AFR][1000 genomes];0.92[AMR][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	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs302337	FGFR1OP2	cis	parietal	SCAN
rs302337	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29881600-29915800	Weak transcription	Brain Substantia Nigra	brain
3	chr12:29887400-29915600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:29888800-29915600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:29890200-29915600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:29890600-29913000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:29894600-29907200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:29895000-29910000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:29897200-29916000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:29898000-29910000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:29898200-29915800	Weak transcription	Liver	Liver
12	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:29900400-29907200	Strong transcription	Adipose Nuclei	Adipose
14	chr12:29900600-29908400	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:29901200-29907600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:29901200-29915800	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:29901600-29911600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:29902000-29906800	Strong transcription	Brain Anterior Caudate	brain
19	chr12:29902000-29908000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:29902600-29915800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:29903000-29906600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:29903000-29906800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:29903200-29906200	Weak transcription	Right Atrium	heart
24	chr12:29903200-29906400	Genic enhancers	Muscle Satellite Cultured Cells	--
25	chr12:29903200-29911000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:29903600-29906400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:29903600-29907200	Weak transcription	NHEK	skin
28	chr12:29903600-29915200	Weak transcription	Fetal Brain Female	brain
29	chr12:29903800-29915600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:29904000-29906400	Weak transcription	Fetal Heart	heart
31	chr12:29904200-29906800	Enhancers	NHDF-Ad	bronchial
32	chr12:29904200-29908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:29904200-29916000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:29904400-29906800	Strong transcription	Ovary	ovary
36	chr12:29904400-29907200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:29904400-29908600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:29904400-29915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr12:29904400-29916800	Weak transcription	Gastric	stomach
40	chr12:29904600-29906200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:29904600-29907200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:29904600-29907600	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29904800-29906200	Weak transcription	Aorta	Aorta
45	chr12:29904800-29906200	Weak transcription	Fetal Stomach	stomach
46	chr12:29904800-29906200	Weak transcription	Psoas Muscle	Psoas
47	chr12:29904800-29906200	Weak transcription	Right Ventricle	heart
48	chr12:29904800-29906200	Weak transcription	Spleen	Spleen
49	chr12:29904800-29906400	Enhancers	Osteobl	bone
50	chr12:29904800-29907000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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