Variant report

Variant	rs3934459
Chromosome Location	chr4:645279-645280
allele	C/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:3)
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	POLR2A	chr4:645185-645583	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:645141-645436	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr4:645066-645588	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:645256-645306	HEEpiC	esophagus:	n/a
2	chr4:645256-645306	HRCEpiC	kidney:	n/a
3	chr4:645256-645306	NT2-D1	testis:	n/a
4	chr4:645256-645306	NHBE	bronchial:	n/a
5	chr4:645256-645306	AG10803	skin:	n/a
6	chr4:645256-645306	RPTEC	kidney:	n/a
7	chr4:645256-645306	MCF10A-Er-Src	breast:	n/a
8	chr4:645256-645306	NH-A	brain:	n/a
9	chr4:645256-645306	ProgFib	skin:	n/a
10	chr4:645256-645306	NHDF-neo	bronchial:	n/a
11	chr4:645256-645306	LNCaP	prostate:	n/a
12	chr4:645256-645306	HCT-116	colon:	n/a
13	chr4:645256-645306	SK-N-SH_RA	brain:	n/a
14	chr4:645256-645306	NB4	blood:	n/a
15	chr4:645256-645306	HRE	kidney:	n/a
16	chr4:645256-645306	HAEpiC	amniotic membrane:	n/a
17	chr4:645256-645306	HCM	heart:	n/a
18	chr4:645256-645306	U87	brain:	n/a
19	chr4:645256-645306	AG04449	skin:	fetal
20	chr4:645256-645306	HepG2	liver:	n/a
21	chr4:645256-645306	GM19239	blood:	n/a
22	chr4:645256-645306	BJ	skin:	n/a
23	chr4:645256-645306	Hepatocyte	liver:	n/a
24	chr4:645256-645306	Jurkat	blood:	n/a
25	chr4:645256-645306	CMK	blood:	n/a
26	chr4:645256-645306	ovcar-3	ovarian:	n/a
27	chr4:645256-645306	AG04450	lung:	fetal
28	chr4:645256-645306	HNPCEpiC	eye:	n/a
29	chr4:645256-645306	GM12878	blood:	n/a
30	chr4:645256-645306	AoSMC	blood vessel:	n/a
31	chr4:645256-645306	HEK293	kidney:	embryo
32	chr4:645256-645306	Hela-S3	cervix:	n/a
33	chr4:645256-645306	PrEC	prostate:	n/a
34	chr4:645256-645306	HCF	heart:	n/a
35	chr4:645256-645306	SK-N-SH	brain:	n/a
36	chr4:645256-645306	SK-N-MC	brain:	n/a
37	chr4:645256-645306	IMR90	lung:	fetal
38	chr4:645256-645306	HUVEC	blood vessel:	n/a
39	chr4:645256-645306	AG09309	skin:	n/a
40	chr4:645256-645306	PANC-1	pancreas:	n/a
41	chr4:645256-645306	SKMC	muscle:	n/a
42	chr4:645256-645306	GM06990	blood:	n/a
43	chr4:645256-645306	GM12891	blood:	n/a
44	chr4:645256-645306	GM12892	blood:	n/a
45	chr4:645256-645306	PFSK-1	brain:	n/a
46	chr4:645256-645306	AG09319	gingival:	n/a
47	chr4:645256-645306	MCF-7	breast:	n/a
48	chr4:645256-645306	HL-60	blood:	n/a
49	chr4:645256-645306	Caco-2	colon:	n/a
50	chr4:645256-645306	SAEC	small airway:	n/a

(count:3 , 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	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

No data

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

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10007497	0.82[EUR][1000 genomes]
rs10023472	0.83[ASN][1000 genomes]
rs10027866	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10029928	0.82[EUR][1000 genomes]
rs10031745	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10031968	0.81[EUR][1000 genomes]
rs10033239	0.83[AFR][1000 genomes]
rs1135375	0.82[AMR][1000 genomes]
rs13107358	0.81[EUR][1000 genomes]
rs28374488	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28403281	0.82[EUR][1000 genomes]
rs28438498	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28476575	0.82[EUR][1000 genomes]
rs28502612	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28504161	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28520978	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28568555	0.93[AFR][1000 genomes]
rs28588872	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28600205	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28630797	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28714509	0.82[EUR][1000 genomes]
rs28742899	0.82[AMR][1000 genomes]
rs28754797	0.82[EUR][1000 genomes]
rs28769407	0.82[EUR][1000 genomes]
rs34307246	0.82[EUR][1000 genomes]
rs3864130	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3864131	0.90[AFR][1000 genomes]
rs4075653	0.82[EUR][1000 genomes]
rs4505760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60316402	0.83[AFR][1000 genomes]
rs67030464	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67703486	0.82[EUR][1000 genomes]
rs71602496	0.93[AFR][1000 genomes]
rs72613108	0.83[ASN][1000 genomes]
rs7438471	0.82[EUR][1000 genomes]
rs9884240	0.82[EUR][1000 genomes]
rs9992641	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9997286	0.82[EUR][1000 genomes]
rs9998967	0.82[EUR][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

No data

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	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:643000-646000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:643200-646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:644400-645400	Enhancers	Fetal Heart	heart
12	chr4:644400-646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:644600-645400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr4:644600-645800	Enhancers	Gastric	stomach
15	chr4:644600-646200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:644800-645400	Active TSS	Brain Angular Gyrus	brain
17	chr4:644800-645800	Enhancers	Pancreas	Pancrea
18	chr4:645000-645400	Enhancers	Brain Hippocampus Middle	brain
19	chr4:645000-645600	Active TSS	Brain Anterior Caudate	brain
20	chr4:645000-645600	Bivalent/Poised TSS	HepG2	liver
21	chr4:645000-646000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:645000-648200	Weak transcription	Esophagus	oesophagus
23	chr4:645200-645400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:645200-645400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:645200-645400	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr4:645200-645400	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr4:645200-645400	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr4:645200-645400	Bivalent Enhancer	Fetal Lung	lung
29	chr4:645200-645400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr4:645200-645400	Enhancers	Right Ventricle	heart
31	chr4:645200-645400	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr4:645200-645600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
33	chr4:645200-645800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:645200-646600	Active TSS	Brain Substantia Nigra	brain

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