Variant report

Variant	rs62109743
Chromosome Location	chr19:36544765-36544766
allele	C/G
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	USF1	chr19:36544706-36545678	K562	blood:	n/a	chr19:36545313-36545326 chr19:36545219-36545228 chr19:36545314-36545323 chr19:36545313-36545324 chr19:36545315-36545324 chr19:36545316-36545325 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545218-36545227 chr19:36545216-36545229 chr19:36545212-36545233 chr19:36545309-36545330
2	USF1	chr19:36544714-36545579	SK-N-SH_RA	brain:	n/a	chr19:36545313-36545326 chr19:36545219-36545228 chr19:36545314-36545323 chr19:36545313-36545324 chr19:36545315-36545324 chr19:36545316-36545325 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545218-36545227 chr19:36545216-36545229 chr19:36545212-36545233 chr19:36545309-36545330
3	POLR2A	chr19:36544746-36546237	GM12878	blood:	n/a	n/a
4	NRF1	chr19:36544316-36545959	SK-N-SH	brain:	n/a	chr19:36545347-36545358 chr19:36545347-36545361 chr19:36545422-36545436
5	MTA3	chr19:36544285-36546578	GM12878	blood:	n/a	n/a
6	YY1	chr19:36544730-36546385	A549	lung:	n/a	chr19:36545869-36545881 chr19:36545824-36545835 chr19:36545768-36545782
7	SIN3AK20	chr19:36544468-36546603	A549	lung:	n/a	n/a
8	POLR2A	chr19:36544708-36546360	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:36544668-36546183	GM12878	blood:	n/a	n/a
10	RAD21	chr19:36544432-36545679	IMR90	lung:	n/a	chr19:36545515-36545534
11	BHLHE40	chr19:36544643-36545982	GM12878	blood:	n/a	chr19:36545313-36545326 chr19:36545219-36545228 chr19:36545314-36545323 chr19:36545315-36545324 chr19:36545316-36545325 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545218-36545227 chr19:36545216-36545229 chr19:36545212-36545233 chr19:36545309-36545330 chr19:36545817-36545833
12	POLR2A	chr19:36544548-36546602	U87	brain:	n/a	n/a
13	HCFC1	chr19:36544301-36546572	Hela-S3	cervix:	n/a	n/a
14	ATF3	chr19:36544450-36545764	A549	lung:	n/a	chr19:36545015-36545024 chr19:36545315-36545324 chr19:36545315-36545335 chr19:36545218-36545227 chr19:36545666-36545675 chr19:36545304-36545324
15	MYC	chr19:36544497-36544963	MCF10A-Er-Src	breast:	n/a	n/a
16	EBF1	chr19:36544624-36544873	GM12878	blood:	n/a	n/a
17	MAX	chr19:36544501-36546342	K562	blood:	n/a	chr19:36546139-36546149 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545389-36545396 chr19:36545387-36545396 chr19:36545315-36545324 chr19:36546208-36546218 chr19:36545385-36545400 chr19:36545315-36545324
18	MYBL2	chr19:36544763-36546096	HepG2	liver:	n/a	n/a
19	TBP	chr19:36544725-36545681	GM12878	blood:	n/a	n/a
20	EBF1	chr19:36544530-36544895	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:36544631-36546400	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr19:36544307-36546871	A549	lung:	n/a	chr19:36546139-36546149 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545389-36545396 chr19:36545387-36545396 chr19:36546410-36546419 chr19:36545315-36545324 chr19:36546208-36546218 chr19:36545385-36545400 chr19:36545315-36545324
23	MAX	chr19:36544542-36546623	ECC-1	luminal epithelium:	n/a	chr19:36546139-36546149 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545389-36545396 chr19:36545387-36545396 chr19:36546410-36546419 chr19:36545315-36545324 chr19:36546208-36546218 chr19:36545385-36545400 chr19:36545315-36545324
24	GATA2	chr19:36544470-36545664	SH-SY5Y	brain:	n/a	n/a
25	PML	chr19:36544751-36546392	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:36544733-36546037	GM12878	blood:	n/a	n/a
27	YY1	chr19:36544741-36546214	GM12892	blood:	n/a	chr19:36545869-36545881 chr19:36545824-36545835 chr19:36545768-36545782
28	BACH1	chr19:36544556-36546602	H1-hESC	embryonic stem cell:	n/a	n/a
29	SP1	chr19:36544709-36545906	GM12878	blood:	n/a	chr19:36545013-36545025 chr19:36544980-36544992 chr19:36545692-36545713 chr19:36545189-36545198 chr19:36545394-36545408 chr19:36544981-36544990 chr19:36545686-36545700 chr19:36545189-36545198 chr19:36545014-36545023 chr19:36545665-36545674 chr19:36544981-36544991 chr19:36544998-36545012 chr19:36544980-36544992 chr19:36545665-36545674 chr19:36544997-36545009 chr19:36545014-36545023 chr19:36545664-36545676 chr19:36545666-36545675 chr19:36545189-36545199 chr19:36545015-36545024 chr19:36545190-36545199 chr19:36545664-36545676 chr19:36545013-36545025 chr19:36545188-36545200
30	POLR2A	chr19:36544729-36545589	HUVEC	blood vessel:	n/a	n/a
31	SIN3AK20	chr19:36544744-36545367	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:36544751-36545952	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr19:36544690-36546447	SK-N-SH	brain:	n/a	n/a
34	MAZ	chr19:36544397-36546676	IMR90	lung:	n/a	chr19:36546139-36546149 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545389-36545396 chr19:36545387-36545396 chr19:36546410-36546419 chr19:36545315-36545324 chr19:36546208-36546218 chr19:36545385-36545400 chr19:36545315-36545324
35	POLR2A	chr19:36544597-36546180	PBDE	blood:	n/a	n/a
36	POLR2A	chr19:36544733-36546499	ECC-1	luminal epithelium:	n/a	n/a
37	SIX5	chr19:36544269-36546851	A549	lung:	n/a	n/a
38	POLR2A	chr19:36544529-36546432	GM12892	blood:	n/a	n/a
39	YY1	chr19:36544684-36545013	SK-N-SH_RA	brain:	n/a	n/a
40	RUNX3	chr19:36544582-36546123	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:36544697-36546168	GM19193	blood:	n/a	n/a
42	POLR2A	chr19:36544632-36546161	GM12892	blood:	n/a	n/a
43	POLR2A	chr19:36544736-36546465	K562	blood:	n/a	n/a
44	CHD2	chr19:36544721-36546434	Hela-S3	cervix:	n/a	n/a
45	GABPA	chr19:36544325-36544952	A549	lung:	n/a	n/a
46	POLR2A	chr19:36544705-36546285	GM12891	blood:	n/a	n/a
47	MAX	chr19:36544566-36546459	K562	blood:	n/a	chr19:36546139-36546149 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545389-36545396 chr19:36545387-36545396 chr19:36546410-36546419 chr19:36545315-36545324 chr19:36546208-36546218 chr19:36545385-36545400 chr19:36545315-36545324
48	BHLHE40	chr19:36544578-36546139	K562	blood:	n/a	chr19:36545313-36545326 chr19:36545219-36545228 chr19:36545314-36545323 chr19:36545315-36545324 chr19:36545316-36545325 chr19:36545315-36545324 chr19:36545218-36545227 chr19:36545218-36545227 chr19:36545216-36545229 chr19:36545212-36545233 chr19:36545309-36545330 chr19:36545817-36545833
49	CREB1	chr19:36544732-36546504	A549	lung:	n/a	n/a
50	SIN3AK20	chr19:36544636-36546281	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36485209..36487448-chr19:36544116..36546055,2	MCF-7	breast:
2	chr19:36503789..36506155-chr19:36544255..36546130,2	K562	blood:
3	chr19:36544745..36545679-chr3:48956268..48957255,2	Hela-S3	cervix:
4	chr19:36497884..36507784-chr19:36542079..36547610,17	MCF-7	breast:
5	chr19:36393181..36395162-chr19:36544398..36547293,2	K562	blood:
6	chr19:36544216..36546740-chr19:36604520..36606743,4	K562	blood:
7	chr19:36484527..36490376-chr19:36543488..36547183,11	K562	blood:
8	chr19:36544227..36545755-chr8:126441431..126444271,2	MCF-7	breast:
9	chr19:36543278..36547003-chr19:36629856..36633093,3	MCF-7	breast:
10	chr19:36543835..36550918-chr19:36603651..36608049,11	MCF-7	breast:
11	chr19:36543201..36546500-chr19:36630161..36633757,3	MCF-7	breast:
12	chr19:36544655..36547364-chr19:36630776..36632492,2	K562	blood:
13	chr19:36504655..36506922-chr19:36544255..36547222,4	K562	blood:
14	chr19:36496294..36501686-chr19:36543356..36547257,9	MCF-7	breast:
15	chr19:36543772..36546988-chr19:36561665..36565427,3	MCF-7	breast:
16	chr19:36333824..36336431-chr19:36543842..36546200,2	MCF-7	breast:
17	chr19:36034751..36036442-chr19:36544192..36546126,2	K562	blood:
18	chr19:36502189..36508386-chr19:36540645..36546835,9	MCF-7	breast:

Variant related genes	Relation type
WDR62	TF binding region
ENSG00000126247	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000126264	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000239382	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000267698	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10414679	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10418015	0.83[EUR][1000 genomes]
rs10423651	0.96[ASN][1000 genomes]
rs10425692	0.96[ASN][1000 genomes]
rs10426582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12462432	0.88[ASN][1000 genomes]
rs12462632	0.94[ASN][1000 genomes]
rs12462674	0.90[ASN][1000 genomes]
rs12972660	0.85[AMR][1000 genomes]
rs12976505	0.80[ASN][1000 genomes]
rs12977802	0.86[AMR][1000 genomes]
rs12977814	0.80[ASN][1000 genomes]
rs12978482	0.80[ASN][1000 genomes]
rs12979093	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2023865	0.96[ASN][1000 genomes]
rs2072606	0.80[AMR][1000 genomes]
rs2075474	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2079151	0.81[ASN][1000 genomes]
rs34906485	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35125548	0.96[ASN][1000 genomes]
rs35875194	0.98[ASN][1000 genomes]
rs3826995	0.87[ASN][1000 genomes]
rs4461192	0.91[ASN][1000 genomes]
rs4805154	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4805155	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4806252	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4806253	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4806279	0.80[AMR][1000 genomes]
rs4806280	0.85[AMR][1000 genomes]
rs56034793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721542	0.96[ASN][1000 genomes]
rs7245762	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247057	0.83[EUR][1000 genomes]
rs7250448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7257383	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259592	0.91[ASN][1000 genomes]
rs7260609	0.88[ASN][1000 genomes]
rs8100250	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8103569	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36543600-36544800	Flanking Active TSS	Dnd41	blood
2	chr19:36543600-36546800	Active TSS	Fetal Kidney	kidney
3	chr19:36543600-36547000	Active TSS	NHDF-Ad	bronchial
4	chr19:36543800-36545000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:36543800-36546400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr19:36544000-36545000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr19:36544000-36545000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr19:36544000-36545800	Active TSS	Colonic Mucosa	Colon
9	chr19:36544000-36546000	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr19:36544000-36546000	Active TSS	Fetal Brain Male	brain
11	chr19:36544000-36546000	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:36544000-36546400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:36544000-36546400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:36544200-36544800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:36544200-36544800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr19:36544200-36544800	Flanking Active TSS	Fetal Thymus	thymus
17	chr19:36544200-36545000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr19:36544200-36545000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr19:36544200-36545000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr19:36544200-36545000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:36544200-36545800	Active TSS	Right Ventricle	heart
22	chr19:36544200-36545800	Active TSS	Stomach Smooth Muscle	stomach
23	chr19:36544200-36546000	Active TSS	Fetal Intestine Small	intestine
24	chr19:36544200-36546000	Active TSS	Fetal Lung	lung
25	chr19:36544200-36546200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:36544200-36546200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36544200-36546200	Active TSS	Brain Germinal Matrix	brain
28	chr19:36544200-36546200	Active TSS	Duodenum Mucosa	Duodenum
29	chr19:36544200-36546400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:36544200-36546400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:36544200-36546400	Active TSS	Muscle Satellite Cultured Cells	--
32	chr19:36544200-36546600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:36544200-36546600	Active TSS	Psoas Muscle	Psoas
34	chr19:36544200-36546800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:36544200-36546800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:36544200-36546800	Active TSS	HSMM	muscle
37	chr19:36544200-36547600	Active TSS	NHLF	lung
38	chr19:36544400-36544800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr19:36544400-36544800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr19:36544400-36544800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr19:36544400-36544800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr19:36544400-36544800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:36544400-36544800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr19:36544400-36544800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:36544400-36544800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr19:36544400-36544800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:36544400-36544800	Flanking Active TSS	Placenta	Placenta
48	chr19:36544400-36544800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:36544400-36544800	Flanking Active TSS	Thymus	Thymus
50	chr19:36544400-36544800	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links