Variant report

Variant	rs2350530
Chromosome Location	chr12:29619577-29619578
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	chr12:29617945..29620582-chr5:127531925..127533690,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10771535	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771537	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843424	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10843425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843426	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1347570	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1436317	0.85[EUR][1000 genomes]
rs1436318	0.85[EUR][1000 genomes]
rs2043623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2060570	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487822	0.86[EUR][1000 genomes]
rs7296963	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2350530	RP11-996F15.2	cis	Thyroid	GTEx
rs2350530	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2350530	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs2350530	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs2350530	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29584200-29641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:29588000-29639800	Weak transcription	Aorta	Aorta
3	chr12:29598400-29657400	Weak transcription	HSMM	muscle
4	chr12:29600000-29639800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
6	chr12:29604200-29655400	Weak transcription	Adipose Nuclei	Adipose
7	chr12:29608200-29622000	Weak transcription	Brain Anterior Caudate	brain
8	chr12:29608600-29624800	Weak transcription	Pancreas	Pancrea
9	chr12:29608800-29627200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:29609400-29631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:29612800-29655600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:29613600-29655600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:29613600-29666800	Weak transcription	Spleen	Spleen
14	chr12:29614400-29622200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:29614600-29658000	Weak transcription	HSMMtube	muscle
16	chr12:29615000-29624600	Weak transcription	Left Ventricle	heart
17	chr12:29616400-29659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:29617400-29657400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:29618200-29642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:29619400-29621000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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