Variant report

Variant	rs28374488
Chromosome Location	chr4:644815-644816
allele	A/G
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:4)
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	FOXA1	chr4:644734-644994	HepG2	liver:	n/a	n/a
2	FOXA1	chr4:644686-645187	HepG2	liver:	n/a	n/a
3	FOXA1	chr4:644781-645158	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:644805-644855	GM12891	blood:	n/a
2	chr4:644805-644855	Jurkat	blood:	n/a
3	chr4:644805-644855	AG04449	skin:	fetal
4	chr4:644805-644855	HCPEpiC	choroid plexus:	n/a
5	chr4:644805-644855	MCF-7	breast:	n/a
6	chr4:644805-644855	NH-A	brain:	n/a
7	chr4:644805-644855	HCT-116	colon:	n/a
8	chr4:644805-644855	GM12892	blood:	n/a
9	chr4:644805-644855	SK-N-SH	brain:	n/a
10	chr4:644805-644855	HCF	heart:	n/a
11	chr4:644805-644855	HepG2	liver:	n/a
12	chr4:644805-644855	PrEC	prostate:	n/a
13	chr4:644805-644855	AG10803	skin:	n/a
14	chr4:644805-644855	HNPCEpiC	eye:	n/a
15	chr4:644805-644855	HEEpiC	esophagus:	n/a
16	chr4:644805-644855	ECC-1	luminal epithelium:	n/a
17	chr4:644805-644855	LNCaP	prostate:	n/a
18	chr4:644805-644855	BJ	skin:	n/a
19	chr4:644805-644855	PANC-1	pancreas:	n/a
20	chr4:644805-644855	A549	lung:	n/a
21	chr4:644805-644855	SK-N-MC	brain:	n/a
22	chr4:644805-644855	MCF10A-Er-Src	breast:	n/a
23	chr4:644805-644855	Hela-S3	cervix:	n/a
24	chr4:644805-644855	HCM	heart:	n/a
25	chr4:644805-644855	HRPEpiC	eye:	n/a
26	chr4:644805-644855	T-47D	breast:	n/a
27	chr4:644805-644855	AG09319	gingival:	n/a
28	chr4:644805-644855	ProgFib	skin:	n/a
29	chr4:644805-644855	Caco-2	colon:	n/a
30	chr4:644805-644855	NB4	blood:	n/a
31	chr4:644805-644855	GM06990	blood:	n/a
32	chr4:644805-644855	CMK	blood:	n/a
33	chr4:644805-644855	NHBE	bronchial:	n/a
34	chr4:644805-644855	BE2_C	brain:	n/a
35	chr4:644805-644855	HIPEpiC	eye:	n/a
36	chr4:644805-644855	HMEC	breast:	n/a
37	chr4:644805-644855	K562	blood:	n/a
38	chr4:644805-644855	IMR90	lung:	fetal
39	chr4:644805-644855	AG04450	lung:	fetal
40	chr4:644805-644855	PFSK-1	brain:	n/a
41	chr4:644805-644855	AoSMC	blood vessel:	n/a
42	chr4:644805-644855	RPTEC	kidney:	n/a
43	chr4:644805-644855	ovcar-3	ovarian:	n/a
44	chr4:644805-644855	SK-N-SH_RA	brain:	n/a
45	chr4:644805-644855	AG09309	skin:	n/a
46	chr4:644805-644855	SAEC	small airway:	n/a
47	chr4:644805-644855	HAEpiC	amniotic membrane:	n/a
48	chr4:644805-644855	HRE	kidney:	n/a
49	chr4:644805-644855	HRCEpiC	kidney:	n/a
50	chr4:644805-644855	HL-60	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:644808..646339-chr4:648173..650037,2	K562	blood:
2	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:
3	chr4:642131..644821-chr4:649750..652284,2	MCF-7	breast:
4	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

No data

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

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10007206	0.93[ASN][1000 genomes]
rs10007497	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10011154	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10021714	0.80[CHD][hapmap]
rs10023472	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[ASN][1000 genomes]
rs10027866	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029928	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031745	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031968	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10033239	0.83[AFR][1000 genomes]
rs11248029	0.89[ASN][1000 genomes]
rs1135375	0.80[AMR][1000 genomes]
rs13107358	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28380593	0.91[ASN][1000 genomes]
rs28403281	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28438498	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]
rs28476575	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28502612	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28504161	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28520978	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28568555	0.92[AFR][1000 genomes]
rs28583078	0.82[ASW][hapmap];0.84[MKK][hapmap]
rs28588872	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600205	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28630797	0.90[AFR][1000 genomes]
rs28675771	0.81[YRI][hapmap]
rs28714509	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28742899	0.80[AMR][1000 genomes]
rs28754797	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28769407	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28826275	0.89[ASN][1000 genomes]
rs34307246	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3864130	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3864131	0.89[AFR][1000 genomes]
rs3888807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3891250	0.88[ASW][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs3934459	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4075653	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4505760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59623849	0.92[ASN][1000 genomes]
rs60316402	0.82[AFR][1000 genomes]
rs67030464	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67703486	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71602496	0.92[AFR][1000 genomes]
rs72611195	0.82[ASN][1000 genomes]
rs72611197	0.88[ASN][1000 genomes]
rs72611198	0.89[ASN][1000 genomes]
rs72611199	0.89[ASN][1000 genomes]
rs72611200	0.89[ASN][1000 genomes]
rs72611201	0.89[ASN][1000 genomes]
rs72611202	0.89[ASN][1000 genomes]
rs72613103	0.89[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	0.85[MKK][hapmap]
rs7438471	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7661376	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs9884240	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9992641	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9997286	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9998967	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]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28374488	POLN	cis	parietal	SCAN
rs28374488	MYOZ3	trans	parietal	SCAN
rs28374488	ZNF141	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:642600-645000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:643000-646000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:643200-646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:644000-645200	Enhancers	Brain Substantia Nigra	brain
13	chr4:644200-645000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:644400-645000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:644400-645200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
16	chr4:644400-645400	Enhancers	Fetal Heart	heart
17	chr4:644400-646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:644600-645000	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr4:644600-645000	Enhancers	Esophagus	oesophagus
20	chr4:644600-645000	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr4:644600-645200	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:644600-645400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:644600-645800	Enhancers	Gastric	stomach
24	chr4:644600-646200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:644800-645000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:644800-645000	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr4:644800-645000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:644800-645000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr4:644800-645000	Bivalent Enhancer	Fetal Thymus	thymus
30	chr4:644800-645000	Bivalent Enhancer	Left Ventricle	heart
31	chr4:644800-645000	Flanking Bivalent TSS/Enh	HMEC	breast
32	chr4:644800-645200	Flanking Active TSS	Right Ventricle	heart
33	chr4:644800-645400	Active TSS	Brain Angular Gyrus	brain
34	chr4:644800-645800	Enhancers	Pancreas	Pancrea

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