Variant report

Variant	rs986594
Chromosome Location	chr12:29840026-29840027
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10771568	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10771570	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843474	1.00[JPT][hapmap]
rs10843492	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050347	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050351	0.93[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11050357	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050360	0.86[CHB][hapmap]
rs11050379	0.94[EUR][1000 genomes]
rs11050380	0.94[EUR][1000 genomes]
rs11613403	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834387	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12226911	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823749	0.83[TSI][hapmap]
rs2033030	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2194817	0.93[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759889	0.94[CEU][hapmap];0.92[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs986594	TMTC1	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29816600-29840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:29822400-29840200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:29825400-29847800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29828600-29854000	Weak transcription	Aorta	Aorta
7	chr12:29829800-29841400	Weak transcription	Right Atrium	heart
8	chr12:29829800-29842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:29830000-29842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:29830000-29844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:29830000-29854000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:29830000-29861600	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:29830200-29857400	Weak transcription	HSMM	muscle
14	chr12:29830400-29857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:29830600-29858000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:29830800-29841400	Weak transcription	Left Ventricle	heart
17	chr12:29830800-29862600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:29831400-29850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:29831600-29840600	Weak transcription	Psoas Muscle	Psoas
20	chr12:29835000-29846800	Weak transcription	Right Ventricle	heart
21	chr12:29837600-29842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:29837600-29864200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:29837800-29844000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:29838000-29851800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:29839400-29858400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:29839600-29840600	Weak transcription	Spleen	Spleen

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