Variant report

Variant	rs28682363
Chromosome Location	chr4:571748-571749
allele	G/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	KAP1	chr4:571118-572058	HEK293	kidney:	n/a	chr4:571445-571454
2	POLR2A	chr4:569033-571774	H1-neurons	neurons:	n/a	n/a
3	TAF1	chr4:570746-571792	H1-neurons	neurons:	n/a	n/a
4	SUZ12	chr4:571267-572780	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTBP2	chr4:570834-571856	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr4:568983-572510	H1-neurons	neurons:	n/a	chr4:569243-569263 chr4:569243-569263 chr4:570373-570386 chr4:569178-569198 chr4:569813-569826 chr4:569681-569691 chr4:570404-570417 chr4:571320-571333 chr4:570810-570820 chr4:569251-569261 chr4:569244-569262 chr4:569243-569252 chr4:571381-571394 chr4:569243-569263 chr4:570817-570830 chr4:569248-569257 chr4:569249-569263 chr4:571378-571391 chr4:569728-569741 chr4:569246-569259 chr4:569243-569256 chr4:569731-569744
7	POLR2A	chr4:570768-572264	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:571737-571787	Hela-S3	cervix:	n/a
2	chr4:571737-571787	HIPEpiC	eye:	n/a
3	chr4:571737-571787	AG09319	gingival:	n/a
4	chr4:571737-571787	HRE	kidney:	n/a
5	chr4:571737-571787	SK-N-SH_RA	brain:	n/a
6	chr4:571737-571787	HL-60	blood:	n/a
7	chr4:571737-571787	BE2_C	brain:	n/a
8	chr4:571737-571787	NHDF-neo	bronchial:	n/a
9	chr4:571737-571787	HCT-116	colon:	n/a
10	chr4:571737-571787	PFSK-1	brain:	n/a
11	chr4:571737-571787	HCPEpiC	choroid plexus:	n/a
12	chr4:571737-571787	HPAEpiC	pulmonary alveolar:	n/a
13	chr4:571737-571787	LNCaP	prostate:	n/a
14	chr4:571737-571787	Hepatocyte	liver:	n/a
15	chr4:571737-571787	HAEpiC	amniotic membrane:	n/a
16	chr4:571737-571787	GM06990	blood:	n/a
17	chr4:571737-571787	ovcar-3	ovarian:	n/a
18	chr4:571737-571787	HCM	heart:	n/a
19	chr4:571737-571787	IMR90	lung:	fetal
20	chr4:571737-571787	Jurkat	blood:	n/a
21	chr4:571737-571787	A549	lung:	n/a
22	chr4:571737-571787	HRPEpiC	eye:	n/a
23	chr4:571737-571787	HEK293	kidney:	embryo
24	chr4:571737-571787	GM19239	blood:	n/a
25	chr4:571737-571787	HEEpiC	esophagus:	n/a
26	chr4:571737-571787	AoSMC	blood vessel:	n/a
27	chr4:571737-571787	MCF10A-Er-Src	breast:	n/a
28	chr4:571737-571787	AG04449	skin:	fetal
29	chr4:571737-571787	ProgFib	skin:	n/a
30	chr4:571737-571787	U87	brain:	n/a
31	chr4:571737-571787	PrEC	prostate:	n/a
32	chr4:571737-571787	RPTEC	kidney:	n/a
33	chr4:571737-571787	AG09309	skin:	n/a
34	chr4:571737-571787	H1-hESC	embryonic stem cell:	embryo
35	chr4:571737-571787	ECC-1	luminal epithelium:	n/a
36	chr4:571737-571787	AG10803	skin:	n/a
37	chr4:571737-571787	SK-N-MC	brain:	n/a
38	chr4:571737-571787	HMEC	breast:	n/a
39	chr4:571737-571787	CMK	blood:	n/a
40	chr4:571737-571787	BJ	skin:	n/a
41	chr4:571737-571787	NH-A	brain:	n/a
42	chr4:571737-571787	PANC-1	pancreas:	n/a
43	chr4:571737-571787	HepG2	liver:	n/a
44	chr4:571737-571787	GM12892	blood:	n/a
45	chr4:571737-571787	GM12891	blood:	n/a
46	chr4:571737-571787	AG04450	lung:	fetal
47	chr4:571737-571787	SAEC	small airway:	n/a
48	chr4:571737-571787	NHBE	bronchial:	n/a
49	chr4:571737-571787	NB4	blood:	n/a
50	chr4:571737-571787	SKMC	muscle:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:570799..573548-chr4:580234..582794,2	MCF-7	breast:
2	chr4:560309..561984-chr4:571273..573145,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-1	chr4:570957-572108	ENSG00000256961
2	lnc-PDE6B-1	chr4:571079-572650	NONHSAT094567
3	lnc-PDE6B-1	chr4:571582-574077	NONHSAT094572
4	lnc-PDE6B-1	chr4:571576-571933	NONHSAT094574

Variant related genes	Relation type
ENSG00000273238	TF binding region
ENSG00000273238	CpG island

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10012461	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015198	0.85[EUR][1000 genomes]
rs10018393	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10024575	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13101691	0.85[EUR][1000 genomes]
rs13103955	0.85[EUR][1000 genomes]
rs13107526	0.85[EUR][1000 genomes]
rs13111179	0.85[EUR][1000 genomes]
rs13116523	0.85[EUR][1000 genomes]
rs13117283	0.85[EUR][1000 genomes]
rs13127213	0.89[EUR][1000 genomes]
rs13133935	0.85[EUR][1000 genomes]
rs13136626	0.85[EUR][1000 genomes]
rs13139052	0.82[EUR][1000 genomes]
rs13139089	0.85[EUR][1000 genomes]
rs13147797	0.85[EUR][1000 genomes]
rs13150119	0.85[EUR][1000 genomes]
rs28648408	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28654405	0.85[EUR][1000 genomes]
rs28687729	0.85[EUR][1000 genomes]
rs28710261	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28754934	0.85[EUR][1000 genomes]
rs34053163	0.85[EUR][1000 genomes]
rs34075612	0.85[EUR][1000 genomes]
rs34094325	0.85[EUR][1000 genomes]
rs34096984	0.85[EUR][1000 genomes]
rs34165278	0.85[EUR][1000 genomes]
rs34293668	0.85[EUR][1000 genomes]
rs34363025	0.85[EUR][1000 genomes]
rs34366493	0.85[EUR][1000 genomes]
rs34391278	0.85[EUR][1000 genomes]
rs34402770	0.85[EUR][1000 genomes]
rs34421911	0.85[EUR][1000 genomes]
rs34477049	0.85[EUR][1000 genomes]
rs34568772	0.85[EUR][1000 genomes]
rs34585712	0.85[EUR][1000 genomes]
rs34698095	0.85[EUR][1000 genomes]
rs34953355	0.85[EUR][1000 genomes]
rs34992186	0.85[EUR][1000 genomes]
rs35006826	0.85[EUR][1000 genomes]
rs35137658	0.85[EUR][1000 genomes]
rs35158410	0.85[EUR][1000 genomes]
rs35207129	0.85[EUR][1000 genomes]
rs35219160	0.85[EUR][1000 genomes]
rs35270524	0.85[EUR][1000 genomes]
rs35455427	0.85[EUR][1000 genomes]
rs35535457	0.85[EUR][1000 genomes]
rs35564967	0.85[EUR][1000 genomes]
rs35621580	0.85[EUR][1000 genomes]
rs35649145	0.85[EUR][1000 genomes]
rs35694609	0.85[EUR][1000 genomes]
rs35732782	0.85[EUR][1000 genomes]
rs35843044	0.85[EUR][1000 genomes]
rs35853545	0.85[EUR][1000 genomes]
rs35869797	0.85[EUR][1000 genomes]
rs35894204	0.85[EUR][1000 genomes]
rs35896648	0.85[EUR][1000 genomes]
rs35935310	0.85[EUR][1000 genomes]
rs35972513	0.85[EUR][1000 genomes]
rs36060793	0.85[EUR][1000 genomes]
rs36117387	0.85[EUR][1000 genomes]
rs4420926	0.89[ASN][1000 genomes]
rs56291707	0.83[ASN][1000 genomes]
rs57138956	0.94[ASN][1000 genomes]
rs57161616	0.94[ASN][1000 genomes]
rs57794368	0.94[ASN][1000 genomes]
rs59921252	0.94[ASN][1000 genomes]
rs71602477	0.85[EUR][1000 genomes]
rs71602479	0.85[EUR][1000 genomes]
rs71602480	0.85[EUR][1000 genomes]
rs71602481	0.85[EUR][1000 genomes]
rs71602482	0.85[EUR][1000 genomes]
rs71602484	0.85[EUR][1000 genomes]
rs71602486	0.85[EUR][1000 genomes]
rs71602489	0.85[EUR][1000 genomes]
rs71602492	0.85[EUR][1000 genomes]
rs73056528	0.94[ASN][1000 genomes]
rs73056535	0.94[ASN][1000 genomes]
rs73056537	0.94[ASN][1000 genomes]
rs73074224	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73074226	0.94[ASN][1000 genomes]
rs73074229	0.94[ASN][1000 genomes]
rs7657809	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672426	0.85[EUR][1000 genomes]
rs7674091	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7674895	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7685281	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	esv1815184	chr4:568928-575087	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv1816544	chr4:568928-575087	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3339025	chr4:569577-572125	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:567200-572200	Active TSS	Brain Angular Gyrus	brain
2	chr4:568600-571800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:568600-571800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr4:568800-572000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
5	chr4:570200-571800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr4:570200-571800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr4:570200-571800	Bivalent Enhancer	Spleen	Spleen
8	chr4:570200-572200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr4:570200-572800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr4:570200-573200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:570400-571800	Bivalent Enhancer	Esophagus	oesophagus
12	chr4:570400-571800	Bivalent Enhancer	Placenta	Placenta
13	chr4:570400-572200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr4:570600-572000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr4:570800-571800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:570800-571800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:570800-571800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:570800-571800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:570800-571800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
20	chr4:570800-571800	Flanking Bivalent TSS/Enh	NHEK	skin
21	chr4:570800-572200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
22	chr4:570800-572200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
23	chr4:571000-571800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr4:571000-571800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:571000-571800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:571000-572400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr4:571200-571800	Active TSS	Brain Anterior Caudate	brain
28	chr4:571200-571800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
29	chr4:571200-571800	Bivalent Enhancer	Fetal Brain Male	brain
30	chr4:571200-571800	Flanking Bivalent TSS/Enh	HepG2	liver
31	chr4:571200-572000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:571200-572000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
33	chr4:571200-572200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:571200-572400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:571200-572600	Weak transcription	Pancreas	Pancrea
36	chr4:571200-573600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr4:571400-571800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:571400-571800	Bivalent Enhancer	Colonic Mucosa	Colon
39	chr4:571400-571800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr4:571400-571800	Bivalent Enhancer	Fetal Stomach	stomach
41	chr4:571400-571800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
42	chr4:571400-572000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr4:571400-572000	Bivalent Enhancer	Right Ventricle	heart
44	chr4:571400-572400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:571400-572800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
46	chr4:571600-571800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:571600-571800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:571600-571800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr4:571600-571800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:571600-571800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links