Variant report

Variant	rs2213163
Chromosome Location	chr12:48390585-48390586
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48384703..48387276-chr12:48389834..48391406,2	K562	blood:
2	chr12:48346353..48348105-chr12:48388384..48390746,2	MCF-7	breast:
3	chr12:48390214..48392047-chr12:48396336..48398947,2	K562	blood:
4	chr12:48387141..48389064-chr12:48389409..48391360,2	MCF-7	breast:
5	chr12:48389851..48391861-chr12:48407332..48409151,2	MCF-7	breast:
6	chr12:48389997..48392047-chr12:48397447..48399843,2	K562	blood:
7	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10875714	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10875715	0.92[EUR][1000 genomes]
rs12228854	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12308909	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2023939	0.96[ASN][1000 genomes]
rs2213162	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2226946	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2248990	0.92[ASN][1000 genomes]
rs2276453	0.95[ASN][1000 genomes]
rs2898056	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3737548	0.80[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782915	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3809322	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3809324	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56037230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56959315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740022	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2213163	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2213163	ZNF641	cis	Muscle Skeletal	GTEx
rs2213163	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs2213163	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
9	chr12:48389000-48390600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:48389000-48390600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr12:48389200-48391000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:48389400-48390600	Enhancers	Fetal Brain Female	brain
13	chr12:48389400-48390600	Enhancers	Fetal Lung	lung
14	chr12:48389400-48390600	Enhancers	Fetal Muscle Leg	muscle
15	chr12:48389400-48390600	Enhancers	HSMMtube	muscle
16	chr12:48389400-48391000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:48389800-48391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:48389800-48391800	Enhancers	Liver	Liver
19	chr12:48390000-48395000	Weak transcription	Right Atrium	heart
20	chr12:48390200-48391000	Weak transcription	Fetal Intestine Small	intestine
21	chr12:48390200-48391200	Weak transcription	Placenta	Placenta
22	chr12:48390200-48391800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:48390400-48394600	Weak transcription	Left Ventricle	heart
24	chr12:48390400-48394600	Weak transcription	Right Ventricle	heart

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