Variant report

Variant	rs11050428
Chromosome Location	chr12:29931784-29931785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29926045..29928762-chr12:29929311..29931905,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10771578	0.82[AMR][1000 genomes]
rs302338	0.81[CHB][hapmap]
rs876534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11050428	TMTC1	cis	multi-tissue	Pritchard
rs11050428	TMTC1	cis	Whole Blood	GTEx
rs11050428	FGFR1OP2	cis	parietal	SCAN
rs11050428	FGD4	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
2	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:29922600-29934000	Weak transcription	NHLF	lung
4	chr12:29922800-29933800	Weak transcription	Hela-S3	cervix
5	chr12:29925400-29934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:29925600-29934200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:29927200-29931800	Weak transcription	Right Atrium	heart
8	chr12:29927200-29931800	Weak transcription	Right Ventricle	heart
9	chr12:29927200-29931800	Weak transcription	Spleen	Spleen
10	chr12:29928800-29934800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:29929200-29931800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29929200-29931800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:29929200-29931800	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:29929200-29932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:29929400-29932800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:29929400-29932800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:29929400-29933200	Weak transcription	HMEC	breast
18	chr12:29929800-29931800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:29929800-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:29929800-29933800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:29930000-29931800	Weak transcription	Left Ventricle	heart
22	chr12:29930000-29934200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:29930000-29934200	Weak transcription	HSMM	muscle
24	chr12:29930800-29932200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:29930800-29932800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:29930800-29933600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:29930800-29934400	Weak transcription	HSMMtube	muscle
28	chr12:29931000-29932200	Enhancers	Colon Smooth Muscle	Colon
29	chr12:29931000-29932400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:29931200-29932200	Enhancers	Aorta	Aorta
31	chr12:29931400-29932000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:29931400-29932200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:29931400-29932400	Enhancers	Ovary	ovary
34	chr12:29931400-29932400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:29931400-29932600	Enhancers	Fetal Heart	heart
36	chr12:29931400-29934000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:29931600-29932200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:29931600-29932400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:29931600-29932400	Enhancers	Adipose Nuclei	Adipose
40	chr12:29931600-29932600	Enhancers	Psoas Muscle	Psoas
41	chr12:29931600-29933600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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