Variant report

Variant	rs2872084
Chromosome Location	chr19:35896298-35896299
allele	A/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	JUN	chr19:35896100-35896632	K562	blood:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
2	EGR1	chr19:35896139-35896376	K562	blood:	n/a	chr19:35896228-35896238 chr19:35896227-35896237
3	CTCF	chr19:35896182-35896341	GM12878	blood:	n/a	n/a
4	CBX3	chr19:35895999-35896376	K562	blood:	n/a	n/a
5	MAX	chr19:35896108-35896308	HepG2	liver:	n/a	n/a
6	YY1	chr19:35896017-35896570	GM12878	blood:	n/a	chr19:35896240-35896256 chr19:35896228-35896237
7	MAX	chr19:35895997-35896689	GM12878	blood:	n/a	n/a
8	TEAD4	chr19:35896093-35896635	K562	blood:	n/a	chr19:35896551-35896560
9	PAX5	chr19:35896089-35896482	GM12878	blood:	n/a	n/a
10	IRF4	chr19:35895900-35896669	GM12878	blood:	n/a	n/a
11	MTA3	chr19:35895817-35896609	GM12878	blood:	n/a	n/a
12	BHLHE40	chr19:35896200-35896490	HepG2	liver:	n/a	n/a
13	RUNX3	chr19:35895948-35896707	GM12878	blood:	n/a	n/a
14	MAX	chr19:35896152-35896344	K562	blood:	n/a	n/a
15	SMC3	chr19:35896242-35896432	Hela-S3	cervix:	n/a	n/a
16	PAX5	chr19:35896184-35896446	GM12878	blood:	n/a	n/a
17	IKZF1	chr19:35896000-35896711	GM12878	blood:	n/a	n/a
18	BHLHE40	chr19:35896093-35896527	K562	blood:	n/a	n/a
19	STAT3	chr19:35895956-35896585	GM12878	blood:	n/a	n/a
20	FOSL2	chr19:35896100-35896434	HepG2	liver:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
21	MAZ	chr19:35896049-35896531	GM12878	blood:	n/a	n/a
22	EBF1	chr19:35896140-35896530	GM12878	blood:	n/a	n/a
23	CREB1	chr19:35895985-35896768	GM12878	blood:	n/a	n/a
24	EBF1	chr19:35896070-35896612	GM12878	blood:	n/a	n/a
25	MYC	chr19:35896046-35896674	MCF10A-Er-Src	breast:	n/a	n/a
26	RELA	chr19:35896109-35896563	GM12891	blood:	n/a	n/a
27	POLR2A	chr19:35895985-35896555	GM12892	blood:	n/a	n/a
28	MEF2A	chr19:35896030-35896553	GM12878	blood:	n/a	n/a
29	FOS	chr19:35896070-35896674	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
30	FOS	chr19:35896050-35896659	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
31	YY1	chr19:35896070-35896642	GM12878	blood:	n/a	chr19:35896240-35896256 chr19:35896228-35896237
32	EP300	chr19:35896089-35896581	GM12878	blood:	n/a	chr19:35896503-35896510
33	NFATC1	chr19:35896042-35896571	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:35895943-35896489	GM12878	blood:	n/a	n/a
35	TCF3	chr19:35896079-35896583	GM12878	blood:	n/a	n/a
36	FOS	chr19:35896065-35896595	MCF10A-Er-Src	breast:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
37	EP300	chr19:35896076-35896565	GM12878	blood:	n/a	chr19:35896503-35896510
38	BATF	chr19:35895947-35896669	GM12878	blood:	n/a	chr19:35896254-35896264 chr19:35896458-35896467
39	ATF2	chr19:35895890-35896658	GM12878	blood:	n/a	n/a
40	POU2F2	chr19:35896090-35896619	GM12891	blood:	n/a	n/a
41	FOSL2	chr19:35895996-35896545	SK-N-SH	brain:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238
42	STAT3	chr19:35896044-35896657	MCF10A-Er-Src	breast:	n/a	n/a
43	BCLAF1	chr19:35896011-35896657	GM12878	blood:	n/a	chr19:35896227-35896236
44	FOXM1	chr19:35895915-35896784	GM12878	blood:	n/a	n/a
45	TCF3	chr19:35896145-35896429	GM12878	blood:	n/a	n/a
46	POU2F2	chr19:35896149-35896559	GM12878	blood:	n/a	n/a
47	STAT5A	chr19:35895851-35896570	GM12878	blood:	n/a	n/a
48	RELA	chr19:35896104-35896539	GM19193	blood:	n/a	n/a
49	PAX5	chr19:35896140-35896487	GM12878	blood:	n/a	n/a
50	JUND	chr19:35896180-35896395	HepG2	liver:	n/a	chr19:35896253-35896261 chr19:35896251-35896263 chr19:35896229-35896238 chr19:35896251-35896262

Variant related genes	Relation type
ENSG00000205786	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11883057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs12971509	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2097682	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35777556	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs386005	0.86[AMR][1000 genomes]
rs4805125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806150	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806151	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4806154	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7252182	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
5	nsv2471	chr19:35837405-35903115	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv833811	chr19:35850257-36029535	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv911626	chr19:35856925-35896467	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv911627	chr19:35856925-35921266	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35886800-35899200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:35894600-35896400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:35894600-35896400	Weak transcription	Adipose Nuclei	Adipose
4	chr19:35894600-35896800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:35894600-35900200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:35894800-35901000	Weak transcription	Right Ventricle	heart
7	chr19:35895200-35897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:35895600-35897000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:35895800-35896600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr19:35895800-35896600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:35895800-35896800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:35895800-35896800	Enhancers	HMEC	breast
13	chr19:35895800-35896800	Enhancers	NHEK	skin
14	chr19:35895800-35897000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:35895800-35897000	Enhancers	NHDF-Ad	bronchial
16	chr19:35895800-35897000	Enhancers	Osteobl	bone
17	chr19:35896000-35896400	Enhancers	Brain Cingulate Gyrus	brain
18	chr19:35896000-35896400	Active TSS	Spleen	Spleen
19	chr19:35896000-35896600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:35896000-35896600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:35896000-35896800	Enhancers	Placenta	Placenta
22	chr19:35896000-35897000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:35896200-35896400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr19:35896200-35896400	Flanking Active TSS	HepG2	liver
25	chr19:35896200-35896600	Enhancers	A549	lung
26	chr19:35896200-35896800	Enhancers	K562	blood
27	chr19:35896200-35898000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links