Variant report

Variant	rs12226911
Chromosome Location	chr12:29841096-29841097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29835864..29838266-chr12:29840927..29842725,2	K562	blood:

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

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

rs_ID	r²[population]
rs10771568	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10771570	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843474	1.00[JPT][hapmap]
rs10843492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11050347	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11050351	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11050357	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11050360	0.86[CHB][hapmap]
rs11050379	0.94[EUR][1000 genomes]
rs11050380	0.94[EUR][1000 genomes]
rs11613403	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11834387	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12823749	0.83[TSI][hapmap]
rs2033030	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2194817	0.86[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3964	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759889	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs986594	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]

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
rs12226911	TMTC1	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:29825400-29847800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:29828600-29854000	Weak transcription	Aorta	Aorta
5	chr12:29829800-29841400	Weak transcription	Right Atrium	heart
6	chr12:29829800-29842800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:29830000-29842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:29830000-29844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:29830000-29854000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:29830000-29861600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:29830200-29857400	Weak transcription	HSMM	muscle
12	chr12:29830400-29857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:29830600-29858000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:29830800-29841400	Weak transcription	Left Ventricle	heart
15	chr12:29830800-29862600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:29831400-29850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:29835000-29846800	Weak transcription	Right Ventricle	heart
18	chr12:29837600-29842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:29837600-29864200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:29837800-29844000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:29838000-29851800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:29839400-29858400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:29840200-29844200	Weak transcription	HMEC	breast
24	chr12:29840600-29841400	Enhancers	Psoas Muscle	Psoas
25	chr12:29840600-29859000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:29840800-29841200	Weak transcription	Spleen	Spleen
27	chr12:29840800-29843800	Weak transcription	H9 Cell Line	embryonic stem cell

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