Variant report

Variant	rs7644862
Chromosome Location	chr3:99297916-99297917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13070310	0.93[ASN][1000 genomes]
rs1851258	0.98[ASN][1000 genomes]
rs1857289	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089983	0.93[ASN][1000 genomes]
rs2342801	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4367103	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4413343	0.93[ASN][1000 genomes]
rs4491947	0.93[ASN][1000 genomes]
rs4594655	0.95[ASN][1000 genomes]
rs6774443	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3422853	chr3:99208019-99342748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7644862	TMTC3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99295400-99298600	Enhancers	Osteobl	bone
2	chr3:99295600-99298600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:99295600-99298600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:99295600-99299200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:99295800-99298600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:99295800-99298600	Enhancers	HUVEC	blood vessel
7	chr3:99295800-99298600	Enhancers	NHDF-Ad	bronchial
8	chr3:99295800-99299200	Enhancers	HSMM	muscle
9	chr3:99296200-99298000	Enhancers	NHLF	lung
10	chr3:99296200-99298600	Enhancers	NH-A	brain
11	chr3:99296800-99298400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:99297400-99298000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:99297400-99298000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:99297400-99298600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:99297600-99298400	Weak transcription	HSMMtube	muscle
16	chr3:99297600-99298400	Enhancers	NHEK	skin
17	chr3:99297600-99298600	Enhancers	HMEC	breast
18	chr3:99297600-99298800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:99297800-99298400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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