Variant report

Variant	rs11050396
Chromosome Location	chr12:29851920-29851921
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10219522	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771569	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs1079365	0.85[CHB][hapmap]
rs10843472	0.80[CHB][hapmap]
rs10843476	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs10843477	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs10843478	0.85[CHB][hapmap]
rs10843479	0.90[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843480	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs10843481	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10843482	0.85[CHB][hapmap]
rs10843484	0.93[AMR][1000 genomes]
rs10843485	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10843490	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050346	0.84[AMR][1000 genomes]
rs11050350	0.91[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs11050359	0.90[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes]
rs11050361	0.90[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes]
rs11050365	0.91[AMR][1000 genomes]
rs11050391	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12368564	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1988266	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57697154	0.82[AMR][1000 genomes]
rs6487843	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6487844	0.82[AMR][1000 genomes]
rs7135501	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs741613	0.90[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes]
rs741614	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs741615	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs741616	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974503	0.91[YRI][hapmap]
rs993994	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv557921	chr12:29843095-29859352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11050396	TMTC1	cis	multi-tissue	Pritchard
rs11050396	MRPS35	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29828600-29854000	Weak transcription	Aorta	Aorta
2	chr12:29830000-29854000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:29830000-29861600	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:29830200-29857400	Weak transcription	HSMM	muscle
5	chr12:29830400-29857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:29830600-29858000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:29830800-29862600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:29837600-29864200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:29839400-29858400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:29840600-29859000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:29848200-29854200	Weak transcription	NHDF-Ad	bronchial
12	chr12:29848200-29855200	Weak transcription	Psoas Muscle	Psoas
13	chr12:29848200-29857200	Weak transcription	Left Ventricle	heart
14	chr12:29849800-29853400	Weak transcription	Adipose Nuclei	Adipose
15	chr12:29850400-29852200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:29850400-29852200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:29850400-29852600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:29850400-29854200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29850800-29852200	Enhancers	HMEC	breast
20	chr12:29851000-29852200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:29851000-29852400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:29851000-29852800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr12:29851200-29852200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:29851200-29852200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:29851400-29852200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:29851400-29852200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:29851600-29852000	Enhancers	Fetal Stomach	stomach
28	chr12:29851600-29852200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr12:29851600-29852200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:29851600-29852200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr12:29851600-29852200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr12:29851600-29852200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:29851800-29852000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:29851800-29852000	Enhancers	Brain Anterior Caudate	brain
35	chr12:29851800-29852200	Active TSS	Fetal Kidney	kidney
36	chr12:29851800-29852200	Enhancers	Osteobl	bone
37	chr12:29851800-29852400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr12:29851800-29852600	Enhancers	Muscle Satellite Cultured Cells	--

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