Variant report

Variant	rs11050351
Chromosome Location	chr12:29822895-29822896
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10771568	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771570	1.00[ASW][hapmap];0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843474	1.00[JPT][hapmap]
rs10843492	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs11050347	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050355	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11050356	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11050357	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050360	0.93[CHB][hapmap]
rs11050379	0.83[EUR][1000 genomes]
rs11050380	0.83[EUR][1000 genomes]
rs11613403	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11834387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12226911	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]
rs12823749	0.81[TSI][hapmap]
rs2033030	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2194817	0.86[ASW][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs3964	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs759889	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs986594	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]

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	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	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv870004	chr12:29762415-29825798	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11050351	TMTC1	cis	multi-tissue	Pritchard
rs11050351	PKP2	cis	cerebellum	SCAN
rs11050351	C12orf72	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29778400-29826000	Weak transcription	Fetal Kidney	kidney
2	chr12:29793400-29826200	Weak transcription	NHLF	lung
3	chr12:29794200-29825600	Weak transcription	Fetal Stomach	stomach
4	chr12:29794200-29825600	Weak transcription	HMEC	breast
5	chr12:29794400-29831800	Weak transcription	Ovary	ovary
6	chr12:29794800-29825600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:29794800-29829400	Weak transcription	Hela-S3	cervix
8	chr12:29803600-29824600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29805600-29824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:29806800-29829200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:29810200-29825400	Weak transcription	HSMMtube	muscle
12	chr12:29810400-29825200	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:29811000-29825200	Weak transcription	Fetal Heart	heart
14	chr12:29813400-29825200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:29813400-29825600	Weak transcription	HSMM	muscle
16	chr12:29813600-29825000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:29814000-29824600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:29814000-29824600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29816200-29825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:29816200-29825200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:29816200-29825600	Weak transcription	Left Ventricle	heart
22	chr12:29816600-29840400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:29820200-29851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:29820400-29844200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:29821000-29827400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:29821200-29825400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:29821200-29825600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:29821200-29829600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:29821400-29828600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:29821400-29829800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:29822200-29825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:29822400-29824800	Weak transcription	Psoas Muscle	Psoas
33	chr12:29822400-29828200	Weak transcription	Aorta	Aorta
34	chr12:29822400-29840200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:29822800-29823000	Enhancers	Right Atrium	heart
36	chr12:29822800-29823000	Enhancers	Spleen	Spleen

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