Variant report

Variant	rs9998967
Chromosome Location	chr4:618720-618721
allele	C/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	CTCF	chr4:618699-619112	K562	blood:	n/a	chr4:618772-618785 chr4:618786-618794
2	RAD21	chr4:618634-619203	H1-hESC	embryonic stem cell:	n/a	chr4:618876-618889
3	RAD21	chr4:618720-619097	H1-hESC	embryonic stem cell:	n/a	chr4:618876-618889
4	RAD21	chr4:618706-619143	H1-hESC	embryonic stem cell:	n/a	chr4:618876-618889

Variant related genes	Relation type
PDE6B	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10007206	0.98[ASN][1000 genomes]
rs10007497	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10011154	0.96[ASN][1000 genomes]
rs10021714	0.87[ASW][hapmap];0.88[CHD][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs10023472	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10027866	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10029928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10031745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10031968	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10033239	0.83[ASN][1000 genomes]
rs11248029	0.96[ASN][1000 genomes]
rs13107358	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374488	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28380593	0.84[ASN][1000 genomes]
rs28403281	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28438498	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28469188	0.93[EUR][1000 genomes]
rs28476575	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28504161	0.96[ASN][1000 genomes]
rs28588872	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28600205	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28711586	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28714509	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28754797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28769407	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28826275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34307246	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3888807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3934459	0.82[EUR][1000 genomes]
rs4075653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4505760	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs59623849	0.95[ASN][1000 genomes]
rs67030464	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67376373	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67703486	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72611195	0.89[ASN][1000 genomes]
rs72611197	0.95[ASN][1000 genomes]
rs72611198	0.96[ASN][1000 genomes]
rs72611199	0.96[ASN][1000 genomes]
rs72611200	0.96[ASN][1000 genomes]
rs72611201	0.96[ASN][1000 genomes]
rs72611202	0.96[ASN][1000 genomes]
rs72613103	0.96[ASN][1000 genomes]
rs72613104	0.98[ASN][1000 genomes]
rs72613105	0.98[ASN][1000 genomes]
rs72613106	0.98[ASN][1000 genomes]
rs72613107	0.97[ASN][1000 genomes]
rs72613108	0.92[ASN][1000 genomes]
rs7438471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661376	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884240	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9997286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription 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 target site	41 gene(s)	inside rSNPs	diseases
8	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
10	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv593205	chr4:601791-623629	Weak transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
16	nsv967276	chr4:615881-624526	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	esv3418296	chr4:616802-619150	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	esv993737	chr4:618112-628837	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9998967	MYOZ3	trans	parietal	SCAN
rs9998967	POLN	cis	parietal	SCAN
rs9998967	ZNF141	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:616800-624200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:617200-619800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:617600-619600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:617600-619800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr4:617600-620000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr4:617600-620200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:617600-620200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:618000-619800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:618200-618800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:618200-618800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:618200-619200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:618200-619200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:618200-619200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:618200-619200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:618200-619600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:618200-619600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:618400-619200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:618400-619200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr4:618600-619200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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