Variant report

Variant	rs2970828
Chromosome Location	chr12:4553669-4553670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10744641	1.00[JPT][hapmap]
rs10849038	1.00[JPT][hapmap]
rs11063099	1.00[JPT][hapmap]
rs11063156	1.00[JPT][hapmap]
rs11610220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11610225	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11611403	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11613495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17177165	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177242	1.00[ASN][1000 genomes]
rs17183633	1.00[ASN][1000 genomes]
rs2970822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2970823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2970829	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970830	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv898616	chr12:4490059-4564613	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv585	chr12:4514249-4559242	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv33276	chr12:4553216-4554993	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2970828	FOXJ2	cis	parietal	SCAN
rs2970828	LRTM2	cis	cerebellum	SCAN
rs2970828	FBXL14	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4548600-4554800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr12:4549600-4558800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:4550000-4553800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:4551000-4559000	Weak transcription	Right Atrium	heart
5	chr12:4551200-4554200	Weak transcription	Psoas Muscle	Psoas
6	chr12:4551600-4556400	Weak transcription	Fetal Brain Male	brain
7	chr12:4551800-4554000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:4551800-4556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:4551800-4559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:4552000-4553800	Enhancers	Dnd41	blood
11	chr12:4552000-4558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:4552600-4554800	Active TSS	Fetal Muscle Leg	muscle
13	chr12:4553000-4554400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
14	chr12:4553200-4553800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:4553400-4554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:4553400-4554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:4553400-4559000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:4553600-4554000	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr12:4553600-4554000	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr12:4553600-4554200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:4553600-4559000	Weak transcription	Fetal Thymus	thymus

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