Variant report

Variant	rs1551930
Chromosome Location	chr12:29933951-29933952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743673	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743674	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771578	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10771579	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771580	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843501	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10843502	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10843503	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843504	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609828	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231167	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810794	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2882467	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs302335	0.84[AMR][1000 genomes]
rs302336	0.84[AMR][1000 genomes]
rs302337	0.84[AMR][1000 genomes]
rs302338	0.85[AMR][1000 genomes]
rs4244848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244849	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931215	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931216	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4931217	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931218	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931219	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931220	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56703053	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs67168837	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7967779	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1551930	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
2	chr12:29922600-29934000	Weak transcription	NHLF	lung
3	chr12:29925400-29934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:29925600-29934200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:29928800-29934800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:29930000-29934200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:29930000-29934200	Weak transcription	HSMM	muscle
8	chr12:29930800-29934400	Weak transcription	HSMMtube	muscle
9	chr12:29931400-29934000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:29932000-29934400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:29932000-29934800	Weak transcription	Liver	Liver
12	chr12:29932200-29934200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:29932200-29934200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:29932200-29934200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:29932400-29934000	Weak transcription	Right Atrium	heart
16	chr12:29932400-29934000	Weak transcription	Right Ventricle	heart
17	chr12:29932400-29934000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:29932400-29934200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:29932400-29934200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:29932400-29934200	Weak transcription	Left Ventricle	heart
21	chr12:29932400-29934800	Weak transcription	Ovary	ovary
22	chr12:29932400-29935200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:29932400-29935200	Weak transcription	Spleen	Spleen
24	chr12:29932800-29935200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:29933000-29934000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:29933000-29937800	Active TSS	Aorta	Aorta
27	chr12:29933200-29934000	Weak transcription	Psoas Muscle	Psoas
28	chr12:29933400-29935000	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:29933600-29934000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:29933600-29934000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:29933600-29934000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:29933600-29934200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:29933600-29934200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:29933600-29934200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:29933600-29934200	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:29933800-29934000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:29933800-29934000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:29933800-29934000	Enhancers	Adipose Nuclei	Adipose
39	chr12:29933800-29934000	Enhancers	Brain Hippocampus Middle	brain
40	chr12:29933800-29934000	Enhancers	Hela-S3	cervix
41	chr12:29933800-29934200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:29933800-29934200	Enhancers	HMEC	breast
43	chr12:29933800-29934400	Enhancers	Fetal Heart	heart
44	chr12:29933800-29937800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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