Variant report

Variant	rs16997972
Chromosome Location	chr4:128460453-128460454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11929869	1.00[AMR][1000 genomes]
rs11931600	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11933107	1.00[AMR][1000 genomes]
rs11933179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11934177	1.00[AMR][1000 genomes]
rs11934725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11939438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11941076	1.00[AMR][1000 genomes]
rs11946033	1.00[AMR][1000 genomes]
rs11946082	1.00[AMR][1000 genomes]
rs1514305	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012450	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1015564	chr4:128394657-128506962	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1017325	chr4:128408370-128509276	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv595387	chr4:128410916-128523964	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16997972	SATB1	trans	lymphoblastoid	seeQTL
rs16997972	FHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128460200-128460600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
2	chr4:128460200-128461000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:128460200-128461000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:128460200-128461400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:128460200-128462600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:128460200-128462800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr4:128460200-128462800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:128460200-128463200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr4:128460200-128463200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:128460400-128461400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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