Variant report

Variant	rs672107
Chromosome Location	chr12:29917266-29917267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10843506	0.80[ASN][1000 genomes]
rs302315	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs302317	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs302321	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34924103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436124	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439639	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs721617	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7312697	0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs672107	TMTC1	cis	Whole Blood	GTEx
rs672107	TMTC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29880000-29921200	Weak transcription	Fetal Kidney	kidney
2	chr12:29898600-29921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29904800-29924200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:29908800-29918800	Weak transcription	Hela-S3	cervix
8	chr12:29908800-29920800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:29908800-29925000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:29910400-29921400	Weak transcription	NHLF	lung
11	chr12:29910600-29921400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:29910600-29921400	Weak transcription	Osteobl	bone
13	chr12:29911000-29919200	Weak transcription	HMEC	breast
14	chr12:29911800-29922200	Weak transcription	Ovary	ovary
15	chr12:29912000-29921400	Weak transcription	Fetal Stomach	stomach
16	chr12:29912800-29924000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:29913200-29918800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:29913600-29917600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:29915600-29918000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr12:29915600-29919800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:29916000-29921800	Weak transcription	HSMMtube	muscle
22	chr12:29916000-29922400	Weak transcription	Esophagus	oesophagus
23	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
24	chr12:29916200-29922400	Weak transcription	Lung	lung
25	chr12:29916400-29919000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:29916400-29919400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:29916400-29919600	Strong transcription	HSMM	muscle
28	chr12:29916400-29920200	Weak transcription	Brain Germinal Matrix	brain
29	chr12:29916400-29920800	Weak transcription	Brain Angular Gyrus	brain
30	chr12:29916400-29920800	Weak transcription	Fetal Lung	lung
31	chr12:29916400-29921800	Weak transcription	Brain Anterior Caudate	brain
32	chr12:29916600-29919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:29916600-29919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:29916600-29921200	Weak transcription	NHDF-Ad	bronchial
35	chr12:29916600-29921400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:29916600-29921400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:29916600-29923000	Weak transcription	Liver	Liver
38	chr12:29916800-29918400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr12:29916800-29919200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:29916800-29919200	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:29916800-29919200	Weak transcription	Left Ventricle	heart
42	chr12:29916800-29919400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:29916800-29921400	Weak transcription	Right Atrium	heart
44	chr12:29916800-29921600	Weak transcription	Fetal Heart	heart
45	chr12:29916800-29922000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:29916800-29922200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:29916800-29924400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:29916800-29925400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:29917000-29918800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:29917000-29918800	Weak transcription	Adipose Nuclei	Adipose

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