Variant report

Variant	rs7799424
Chromosome Location	chr7:64253570-64253571
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr7:64253539-64254141	K562	blood:	n/a	n/a
2	TEAD4	chr7:64253566-64254231	K562	blood:	n/a	n/a

Variant related genes	Relation type
ZNF138	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10255860	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10259858	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10263876	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10949950	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11763550	0.87[ASN][1000 genomes]
rs11772109	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs11773236	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12667450	0.89[ASN][1000 genomes]
rs13223188	0.86[ASN][1000 genomes]
rs1524823	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1568910	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1568911	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2030811	0.87[JPT][hapmap]
rs2863984	0.94[JPT][hapmap]
rs34344248	0.87[ASN][1000 genomes]
rs34812094	0.82[ASN][1000 genomes]
rs35746520	0.82[ASN][1000 genomes]
rs3763507	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs4398786	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs4717226	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4718153	0.88[JPT][hapmap]
rs4718171	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs56799101	0.83[ASN][1000 genomes]
rs59624556	0.89[ASN][1000 genomes]
rs6460205	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs6460206	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs6460212	0.88[JPT][hapmap]
rs6956037	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6957325	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6974633	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6975625	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs6978652	0.97[ASN][1000 genomes]
rs73142738	0.87[ASN][1000 genomes]
rs7798270	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7809122	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs884476	0.80[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
4	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
10	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
13	esv3394685	chr7:64150166-64268675	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
16	nsv888281	chr7:64250409-64295884	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7799424	RP11-460N20.5	cis	lung	GTEx
rs7799424	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs7799424	SEPHS1P1	cis	Thyroid	GTEx
rs7799424	RP11-797H7.3	cis	Artery Tibial	GTEx
rs7799424	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs7799424	RP11-797H7.3	cis	lung	GTEx
rs7799424	RP11-460N20.5	cis	Whole Blood	GTEx
rs7799424	RP11-797H7.3	cis	Thyroid	GTEx
rs7799424	RP11-797H7.3	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64240600-64254200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:64243400-64254400	Weak transcription	Right Atrium	heart
3	chr7:64250200-64253800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:64252600-64253600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:64252600-64254400	Enhancers	HSMMtube	muscle
6	chr7:64253200-64254600	Enhancers	HSMM	muscle
7	chr7:64253400-64253600	Enhancers	K562	blood

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