Variant report

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs167318	0.98[ASN][1000 genomes]
rs186216	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302315	0.86[CEU][hapmap]
rs302321	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs302341	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302344	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs302347	0.98[ASN][1000 genomes]
rs302349	0.93[ASN][1000 genomes]
rs302350	0.99[ASN][1000 genomes]
rs302352	0.97[ASN][1000 genomes]
rs302353	0.97[ASN][1000 genomes]
rs302355	0.98[ASN][1000 genomes]
rs436124	0.90[CEU][hapmap]
rs439639	0.86[CEU][hapmap]
rs654825	0.88[EUR][1000 genomes]
rs675740	0.81[EUR][1000 genomes]
rs721617	0.82[CEU][hapmap]
rs7316162	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv826294	chr12:29934604-29940372	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	esv3400754	chr12:29935710-29938558	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs302340	TMTC1	Cis_1M	lymphoblastoid	RTeQTL
rs302340	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29936400-29938200	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr12:29937200-29945400	Weak transcription	Spleen	Spleen
3	chr12:29937600-29944000	Weak transcription	Gastric	stomach
4	chr12:29937800-29938200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr12:29937800-29938200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:29937800-29938200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr12:29937800-29938200	Enhancers	Hela-S3	cervix
8	chr12:29937800-29938400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:29937800-29938400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr12:29937800-29941000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:29937800-29943800	Weak transcription	Fetal Kidney	kidney
12	chr12:29937800-29944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:29937800-29944200	Weak transcription	H9 Cell Line	embryonic stem cell

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