Variant report

Variant	rs60220392
Chromosome Location	chr19:56092549-56092550
allele	C/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	SP1	chr19:56092109-56092576	GM12878	blood:	n/a	chr19:56092416-56092428 chr19:56092245-56092259 chr19:56092416-56092428 chr19:56092257-56092271 chr19:56092220-56092234 chr19:56092379-56092390 chr19:56092251-56092265 chr19:56092417-56092426 chr19:56092419-56092433 chr19:56092145-56092154
2	PBX3	chr19:56092043-56092602	SK-N-SH	brain:	n/a	n/a
3	POU2F2	chr19:56092108-56092563	GM12878	blood:	n/a	chr19:56092212-56092224
4	POLR2A	chr19:56092005-56092678	GM12892	blood:	n/a	n/a
5	REST	chr19:56092103-56093468	PFSK-1	brain:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
6	POLR2A	chr19:56091920-56092637	HUVEC	blood vessel:	n/a	n/a
7	ELF1	chr19:56092059-56092629	GM12878	blood:	n/a	chr19:56092349-56092358 chr19:56092350-56092359 chr19:56092348-56092359
8	EP300	chr19:56092046-56092625	ECC-1	luminal epithelium:	n/a	n/a
9	HMGN3	chr19:56091949-56092580	K562	blood:	n/a	n/a
10	ELK1	chr19:56092174-56092554	K562	blood:	n/a	n/a
11	GABPA	chr19:56091985-56093713	A549	lung:	n/a	n/a
12	FOSL2	chr19:56092074-56093868	A549	lung:	n/a	n/a
13	MAX	chr19:56091997-56092573	ECC-1	luminal epithelium:	n/a	chr19:56092224-56092234 chr19:56092361-56092371
14	ZNF143	chr19:56092178-56093032	K562	blood:	n/a	chr19:56092241-56092259
15	POLR2A	chr19:56091640-56092656	GM19193	blood:	n/a	n/a
16	GABPA	chr19:56092042-56092778	HL-60	blood:	n/a	n/a
17	JUND	chr19:56092143-56092998	H1-hESC	embryonic stem cell:	n/a	n/a
18	SRF	chr19:56092040-56092580	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr19:56091707-56092814	MCF10A-Er-Src	breast:	n/a	n/a
20	TRIM28	chr19:56092087-56092562	K562	blood:	n/a	n/a
21	REST	chr19:56092062-56093388	ECC-1	luminal epithelium:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
22	NFIC	chr19:56092061-56092596	ECC-1	luminal epithelium:	n/a	n/a
23	PAX5	chr19:56092057-56092587	GM12878	blood:	n/a	n/a
24	GATA3	chr19:56092115-56092613	MCF-7	breast:	n/a	n/a
25	YY1	chr19:56092094-56092558	SK-N-SH_RA	brain:	n/a	chr19:56092424-56092435
26	SP1	chr19:56091471-56093907	A549	lung:	n/a	chr19:56091862-56091876 chr19:56091908-56091917 chr19:56091907-56091919 chr19:56092416-56092428 chr19:56091904-56091918 chr19:56092245-56092259 chr19:56092416-56092428 chr19:56091879-56091893 chr19:56092257-56092271 chr19:56092220-56092234 chr19:56092379-56092390 chr19:56092251-56092265 chr19:56092417-56092426 chr19:56091994-56092008 chr19:56092419-56092433 chr19:56092145-56092154
27	HEY1	chr19:56091933-56092574	K562	blood:	n/a	n/a
28	RCOR1	chr19:56092045-56093086	K562	blood:	n/a	n/a
29	MAZ	chr19:56091119-56093072	IMR90	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
30	POLR2A	chr19:56091898-56092977	HUVEC	blood vessel:	n/a	n/a
31	MAZ	chr19:56091251-56092828	GM12878	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
32	MAZ	chr19:56091415-56093026	K562	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
33	TBL1XR1	chr19:56092163-56092582	K562	blood:	n/a	n/a
34	POLR2A	chr19:56091950-56092681	MCF-7	breast:	n/a	n/a
35	POLR2A	chr19:56092013-56092597	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr19:56091981-56092581	K562	blood:	n/a	n/a
37	ZNF143	chr19:56092176-56092555	Hela-S3	cervix:	n/a	chr19:56092241-56092259
38	MAX	chr19:56091995-56092560	ECC-1	luminal epithelium:	n/a	chr19:56092224-56092234 chr19:56092361-56092371
39	HCFC1	chr19:56092126-56092973	K562	blood:	n/a	n/a
40	SIN3A	chr19:56091344-56093085	H1-hESC	embryonic stem cell:	n/a	n/a
41	BCL3	chr19:56091329-56093788	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
42	POLR2A	chr19:56091364-56092750	A549	lung:	n/a	n/a
43	TCF12	chr19:56091942-56092694	ECC-1	luminal epithelium:	n/a	n/a
44	TEAD4	chr19:56092173-56092579	HepG2	liver:	n/a	n/a
45	REST	chr19:56092150-56093323	HCT-116	colon:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
46	POLR2A	chr19:56091923-56092601	GM12891	blood:	n/a	n/a
47	RELA	chr19:56092085-56092574	GM15510	blood:	n/a	n/a
48	POLR2A	chr19:56092004-56092621	SK-N-SH	brain:	n/a	n/a
49	FOXM1	chr19:56092118-56092559	GM12878	blood:	n/a	n/a
50	BCL3	chr19:56092005-56093793	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359

No.	Distal block	Cell Line	Cell type
1	chr19:56085801..56089181-chr19:56090146..56094195,5	MCF-7	breast:
2	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
3	chr19:56091409..56094452-chr19:56108819..56113428,6	K562	blood:
4	chr19:56089635..56093860-chr19:56114549..56117863,7	MCF-7	breast:
5	chr19:56092293..56094468-chr19:56145098..56146979,2	K562	blood:
6	chr19:56087478..56090277-chr19:56092054..56093869,2	MCF-7	breast:
7	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
8	chr19:55973159..55975306-chr19:56090568..56094014,3	K562	blood:

Variant related genes	Relation type
ENSG00000267730	TF binding region
ZNF579	TF binding region
ENSG00000171443	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000213015	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403462	0.83[ASN][1000 genomes]
rs10451452	0.84[ASN][1000 genomes]
rs1079082	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1079083	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1079084	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1079085	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11084402	0.97[ASN][1000 genomes]
rs11665826	0.97[ASN][1000 genomes]
rs11668725	0.95[ASN][1000 genomes]
rs11668729	0.95[ASN][1000 genomes]
rs11669682	0.97[ASN][1000 genomes]
rs11879347	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610510	0.93[ASN][1000 genomes]
rs12610512	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610709	0.96[ASN][1000 genomes]
rs12610881	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972159	0.97[ASN][1000 genomes]
rs12974617	0.93[ASN][1000 genomes]
rs12978375	0.95[ASN][1000 genomes]
rs12979354	0.97[ASN][1000 genomes]
rs12979366	0.97[ASN][1000 genomes]
rs12980543	0.97[ASN][1000 genomes]
rs2014329	0.86[ASN][1000 genomes]
rs2864433	0.97[ASN][1000 genomes]
rs2902748	0.97[ASN][1000 genomes]
rs34174244	0.97[ASN][1000 genomes]
rs34715654	0.88[ASN][1000 genomes]
rs34937940	0.93[ASN][1000 genomes]
rs35088354	0.88[ASN][1000 genomes]
rs35197282	0.97[ASN][1000 genomes]
rs35522245	0.97[ASN][1000 genomes]
rs35839536	0.97[ASN][1000 genomes]
rs36047579	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71368855	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71368856	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246944	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251733	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	esv3388302	chr19:56088140-56092838	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr19:56090400-56092800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56090800-56092600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:56090800-56092600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:56091000-56092600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:56091000-56092600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:56091000-56092600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:56091000-56092600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:56091000-56092600	Active TSS	Gastric	stomach
11	chr19:56091000-56092600	Active TSS	Psoas Muscle	Psoas
12	chr19:56091000-56092600	Active TSS	Right Atrium	heart
13	chr19:56091000-56092800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:56091000-56092800	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr19:56091000-56092800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr19:56091000-56092800	Active TSS	Fetal Kidney	kidney
17	chr19:56091000-56092800	Active TSS	Rectal Smooth Muscle	rectum
18	chr19:56091000-56092800	Active TSS	HSMMtube	muscle
19	chr19:56091000-56093000	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr19:56091000-56093200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:56091000-56093200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:56091200-56092600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:56091200-56092600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:56091200-56092800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr19:56091200-56092800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:56091200-56092800	Active TSS	Esophagus	oesophagus
27	chr19:56091200-56092800	Active TSS	Lung	lung
28	chr19:56091200-56092800	Active TSS	Ovary	ovary
29	chr19:56091400-56092600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr19:56091400-56092600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:56091400-56092600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:56091400-56092600	Active TSS	Primary T cells from cord blood	blood
33	chr19:56091400-56092600	Active TSS	Brain Hippocampus Middle	brain
34	chr19:56091400-56092600	Active TSS	Colon Smooth Muscle	Colon
35	chr19:56091400-56092600	Active TSS	Fetal Lung	lung
36	chr19:56091400-56092600	Active TSS	Fetal Stomach	stomach
37	chr19:56091400-56092800	Active TSS	Aorta	Aorta
38	chr19:56091400-56092800	Active TSS	Right Ventricle	heart
39	chr19:56091400-56093000	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr19:56091400-56093000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr19:56091400-56093000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:56091600-56092600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:56091600-56092600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr19:56091600-56092600	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:56091600-56092600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr19:56091600-56092600	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr19:56091600-56092600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:56091600-56092600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:56091600-56092600	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr19:56091600-56092600	Active TSS	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links