Variant report

Variant	rs28438498
Chromosome Location	chr4:642899-642900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:642840-642990	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr4:642820-642970	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr4:642883-643005	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:642885-642935	AG04450	lung:	fetal
2	chr4:642885-642935	Jurkat	blood:	n/a
3	chr4:642885-642935	HRPEpiC	eye:	n/a
4	chr4:642885-642935	GM06990	blood:	n/a
5	chr4:642885-642935	HUVEC	blood vessel:	n/a
6	chr4:642885-642935	AG09309	skin:	n/a
7	chr4:642885-642935	ProgFib	skin:	n/a
8	chr4:642885-642935	MCF-7	breast:	n/a
9	chr4:642885-642935	NT2-D1	testis:	n/a
10	chr4:642885-642935	GM12891	blood:	n/a
11	chr4:642885-642935	PANC-1	pancreas:	n/a
12	chr4:642885-642935	GM19239	blood:	n/a
13	chr4:642885-642935	BJ	skin:	n/a
14	chr4:642885-642935	BE2_C	brain:	n/a
15	chr4:642885-642935	Hela-S3	cervix:	n/a
16	chr4:642885-642935	HL-60	blood:	n/a
17	chr4:642885-642935	HRCEpiC	kidney:	n/a
18	chr4:642885-642935	HRE	kidney:	n/a
19	chr4:642885-642935	Hepatocyte	liver:	n/a
20	chr4:642885-642935	PFSK-1	brain:	n/a
21	chr4:642885-642935	HAEpiC	amniotic membrane:	n/a
22	chr4:642885-642935	H1-hESC	embryonic stem cell:	embryo
23	chr4:642885-642935	GM12878	blood:	n/a
24	chr4:642885-642935	HCT-116	colon:	n/a
25	chr4:642885-642935	HEK293	kidney:	embryo
26	chr4:642885-642935	SAEC	small airway:	n/a
27	chr4:642885-642935	AG04449	skin:	fetal
28	chr4:642885-642935	ECC-1	luminal epithelium:	n/a
29	chr4:642885-642935	HCF	heart:	n/a
30	chr4:642885-642935	LNCaP	prostate:	n/a
31	chr4:642885-642935	HNPCEpiC	eye:	n/a
32	chr4:642885-642935	A549	lung:	n/a
33	chr4:642885-642935	Caco-2	colon:	n/a
34	chr4:642885-642935	GM12892	blood:	n/a
35	chr4:642885-642935	ovcar-3	ovarian:	n/a
36	chr4:642885-642935	SK-N-SH	brain:	n/a
37	chr4:642885-642935	SK-N-MC	brain:	n/a
38	chr4:642885-642935	HIPEpiC	eye:	n/a
39	chr4:642885-642935	SK-N-SH_RA	brain:	n/a
40	chr4:642885-642935	NHDF-neo	bronchial:	n/a
41	chr4:642885-642935	HEEpiC	esophagus:	n/a
42	chr4:642885-642935	PrEC	prostate:	n/a
43	chr4:642885-642935	RPTEC	kidney:	n/a
44	chr4:642885-642935	CMK	blood:	n/a
45	chr4:642885-642935	NB4	blood:	n/a
46	chr4:642885-642935	AoSMC	blood vessel:	n/a
47	chr4:642885-642935	HepG2	liver:	n/a
48	chr4:642885-642935	U87	brain:	n/a
49	chr4:642885-642935	K562	blood:	n/a
50	chr4:642885-642935	NH-A	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr4:641525..644066-chr4:652058..654958,2	K562	blood:
2	chr4:642166..643700-chr4:648904..650417,2	MCF-7	breast:
3	chr4:640899..644048-chr4:645918..649470,4	K562	blood:
4	chr4:623895..625703-chr4:641254..643295,2	K562	blood:
5	chr4:636743..639513-chr4:642400..644519,2	MCF-7	breast:
6	chr4:642830..644425-chr4:665822..667972,2	K562	blood:
7	chr4:642131..644821-chr4:649750..652284,2	MCF-7	breast:
8	chr4:642255..644273-chr4:662905..665187,2	K562	blood:
9	chr4:629516..632051-chr4:640070..643057,2	MCF-7	breast:
10	chr4:642559..644121-chr4:666907..669790,2	MCF-7	breast:

No data

Variant related genes	Relation type
PDE6B	TF binding region
PDE6B	CpG island
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction
ENSG00000215375	Chromatin interaction
ENSG00000169020	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007206	0.93[ASN][1000 genomes]
rs10007497	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10011154	0.95[ASN][1000 genomes]
rs10021714	0.84[CHD][hapmap]
rs10023472	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[ASN][1000 genomes]
rs10027866	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029928	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031745	0.93[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031968	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11248029	0.87[ASN][1000 genomes]
rs13107358	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28374488	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28380593	0.91[ASN][1000 genomes]
rs28403281	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28476575	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28502612	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28504161	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28520978	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28588872	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600205	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28714509	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28742899	0.85[MKK][hapmap];0.81[TSI][hapmap]
rs28754797	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28769407	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28826275	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34307246	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3864130	0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3888807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3891250	0.88[MKK][hapmap]
rs3934459	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4075653	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4505760	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59623849	0.92[ASN][1000 genomes]
rs67030464	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67703486	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72611195	0.80[ASN][1000 genomes]
rs72611197	0.86[ASN][1000 genomes]
rs72611198	0.87[ASN][1000 genomes]
rs72611199	0.87[ASN][1000 genomes]
rs72611200	0.87[ASN][1000 genomes]
rs72611201	0.87[ASN][1000 genomes]
rs72611202	0.87[ASN][1000 genomes]
rs72613103	0.87[ASN][1000 genomes]
rs72613104	0.93[ASN][1000 genomes]
rs72613105	0.93[ASN][1000 genomes]
rs72613106	0.93[ASN][1000 genomes]
rs72613107	0.92[ASN][1000 genomes]
rs72613108	0.99[ASN][1000 genomes]
rs7436737	0.89[MKK][hapmap]
rs7438471	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7661376	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9884240	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9992641	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9997286	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9998967	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]

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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv593207	chr4:629437-645300	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3486347	chr4:636402-643400	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3486351	chr4:636802-643300	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28438498	POLN	cis	parietal	SCAN
rs28438498	MYOZ3	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-643800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:642000-643000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:642000-643200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:642000-643400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:642200-643000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:642400-643000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:642600-643000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
13	chr4:642600-643000	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr4:642600-645000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:642800-644600	Weak transcription	Gastric	stomach
16	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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