Variant report

Variant	rs2248990
Chromosome Location	chr12:48388830-48388831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48346353..48348105-chr12:48388384..48390746,2	MCF-7	breast:
2	chr12:48387141..48389064-chr12:48389409..48391360,2	MCF-7	breast:
3	chr12:48375884..48381022-chr12:48386743..48391938,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12308909	0.84[ASN][1000 genomes]
rs1635533	0.89[EUR][1000 genomes]
rs1793953	0.88[EUR][1000 genomes]
rs1793954	0.87[EUR][1000 genomes]
rs2023939	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213162	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2213163	0.92[ASN][1000 genomes]
rs2226946	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276453	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3737548	0.92[ASN][1000 genomes]
rs56037230	0.92[ASN][1000 genomes]
rs56959315	0.92[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	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
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2248990	H1FNT	cis	Muscle Skeletal	GTEx
rs2248990	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:21 , 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	chr12:48385600-48389000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:48385600-48389600	Weak transcription	Right Atrium	heart
8	chr12:48385800-48389600	Weak transcription	Left Ventricle	heart
9	chr12:48385800-48389600	Weak transcription	Lung	lung
10	chr12:48386000-48389600	Weak transcription	Right Ventricle	heart
11	chr12:48386400-48389800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48387000-48391600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:48387600-48389000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:48387600-48390200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:48388000-48391400	Enhancers	Fetal Brain Male	brain
17	chr12:48388600-48389400	Bivalent Enhancer	Fetal Lung	lung
18	chr12:48388600-48389400	Weak transcription	Psoas Muscle	Psoas
19	chr12:48388600-48390400	Enhancers	Brain Germinal Matrix	brain
20	chr12:48388800-48389400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:48388800-48390200	Strong transcription	Fetal Intestine Small	intestine

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