Variant report

Variant	rs12610512
Chromosome Location	chr19:56091475-56091476
allele	A/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	POLR2A	chr19:56091262-56091852	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:56091373-56091576	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:56091435-56091596	A549	lung:	n/a	n/a
4	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
5	MAZ	chr19:56091119-56093072	IMR90	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
6	MAZ	chr19:56091251-56092828	GM12878	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
7	MAZ	chr19:56091415-56093026	K562	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
8	ZNF143	chr19:56091349-56091705	H1-hESC	embryonic stem cell:	n/a	n/a
9	SIN3A	chr19:56091344-56093085	H1-hESC	embryonic stem cell:	n/a	n/a
10	BCL3	chr19:56091329-56093788	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
11	POLR2A	chr19:56091364-56092750	A549	lung:	n/a	n/a
12	POLR2A	chr19:56091407-56091870	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56091377-56092668	ProgFib	skin:	n/a	n/a
14	MAX	chr19:56091376-56093828	A549	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
15	POLR2A	chr19:56091451-56091670	Gliobla	brain:	n/a	n/a
16	STAT5A	chr19:56091474-56091954	GM12878	blood:	n/a	chr19:56091585-56091597 chr19:56091905-56091917
17	ZBTB7A	chr19:56091367-56092783	ECC-1	luminal epithelium:	n/a	n/a
18	ELF1	chr19:56091440-56091844	GM12878	blood:	n/a	chr19:56091645-56091658
19	CHD1	chr19:56091005-56092989	IMR90	lung:	n/a	n/a
20	MAZ	chr19:56091445-56091699	Hela-S3	cervix:	n/a	chr19:56091562-56091572
21	POLR2A	chr19:56091448-56091854	HUVEC	blood vessel:	n/a	n/a
22	ZBTB7A	chr19:56091387-56091786	K562	blood:	n/a	n/a
23	GABPA	chr19:56091429-56091877	A549	lung:	n/a	n/a
24	SIN3AK20	chr19:56091371-56093235	MCF-7	breast:	n/a	n/a
25	ELF1	chr19:56091418-56091848	K562	blood:	n/a	chr19:56091645-56091658
26	POLR2A	chr19:56091001-56092990	PFSK-1	brain:	n/a	n/a
27	ELF1	chr19:56091462-56091652	K562	blood:	n/a	n/a
28	SP1	chr19:56091354-56093918	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
29	POLR2A	chr19:56091259-56093217	SK-N-MC	brain:	n/a	n/a
30	TCF12	chr19:56091437-56093943	A549	lung:	n/a	n/a
31	REST	chr19:56091163-56093146	H1-neurons	neurons:	n/a	chr19:56092008-56092022 chr19:56092206-56092219 chr19:56092435-56092448
32	ZBTB7A	chr19:56091349-56092699	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr19:56091414-56091850	SK-N-SH	brain:	n/a	n/a
34	MXI1	chr19:56091163-56093260	SK-N-SH	brain:	n/a	n/a
35	ZBTB7A	chr19:56091438-56092653	K562	blood:	n/a	n/a
36	REST	chr19:56091220-56091846	A549	lung:	n/a	n/a
37	POLR2A	chr19:56091446-56091794	A549	lung:	n/a	n/a
38	HCFC1	chr19:56091256-56093043	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:56091291-56092783	K562	blood:	n/a	n/a
40	POLR2A	chr19:56091398-56091893	Hela-S3	cervix:	n/a	n/a

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	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
6	chr19:55973159..55975306-chr19:56090568..56094014,3	K562	blood:

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

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10403462	0.81[ASN][1000 genomes]
rs10451452	0.82[ASN][1000 genomes]
rs1079082	0.93[ASN][1000 genomes]
rs1079083	0.93[ASN][1000 genomes]
rs1079084	0.93[ASN][1000 genomes]
rs1079085	0.93[ASN][1000 genomes]
rs11084402	0.95[ASN][1000 genomes]
rs11665826	0.95[ASN][1000 genomes]
rs11668725	0.92[ASN][1000 genomes]
rs11668729	0.92[ASN][1000 genomes]
rs11669682	0.95[ASN][1000 genomes]
rs11879347	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610510	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12610709	0.93[ASN][1000 genomes]
rs12610881	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12972159	0.95[ASN][1000 genomes]
rs12974617	0.99[ASN][1000 genomes]
rs12978375	0.92[ASN][1000 genomes]
rs12979354	0.95[ASN][1000 genomes]
rs12979366	0.95[ASN][1000 genomes]
rs12980543	0.95[ASN][1000 genomes]
rs2014329	0.91[ASN][1000 genomes]
rs2864433	0.95[ASN][1000 genomes]
rs2902748	0.95[ASN][1000 genomes]
rs34174244	0.95[ASN][1000 genomes]
rs34715654	0.86[ASN][1000 genomes]
rs34937940	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35088354	0.86[ASN][1000 genomes]
rs35197282	0.95[ASN][1000 genomes]
rs35522245	0.95[ASN][1000 genomes]
rs35839536	0.95[ASN][1000 genomes]
rs36047579	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60220392	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71368855	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71368856	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246944	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251733	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	esv3423073	chr19:56088190-56091888	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3437537	chr19:56088665-56091513	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56090000-56091600	Weak transcription	Small Intestine	intestine
2	chr19:56090400-56091600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:56090400-56092400	Active TSS	HSMM	muscle
4	chr19:56090400-56092800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:56090800-56091600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:56090800-56091600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:56090800-56091600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:56090800-56091600	Flanking Active TSS	Dnd41	blood
9	chr19:56090800-56091800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr19:56090800-56092400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:56090800-56092600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:56090800-56092600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:56091000-56091600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:56091000-56091600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:56091000-56091600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:56091000-56091600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr19:56091000-56091600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:56091000-56091600	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr19:56091000-56091600	Flanking Active TSS	Fetal Brain Female	brain
22	chr19:56091000-56091600	Flanking Active TSS	HMEC	breast
23	chr19:56091000-56091600	Flanking Active TSS	K562	blood
24	chr19:56091000-56091800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr19:56091000-56091800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:56091000-56091800	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr19:56091000-56091800	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr19:56091000-56091800	Flanking Active TSS	Brain Substantia Nigra	brain
29	chr19:56091000-56091800	Flanking Active TSS	Pancreas	Pancrea
30	chr19:56091000-56092400	Active TSS	H1 Cell Line	embryonic stem cell
31	chr19:56091000-56092400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:56091000-56092400	Active TSS	Muscle Satellite Cultured Cells	--
33	chr19:56091000-56092400	Active TSS	Fetal Intestine Small	intestine
34	chr19:56091000-56092400	Active TSS	Left Ventricle	heart
35	chr19:56091000-56092400	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr19:56091000-56092400	Active TSS	GM12878-XiMat	blood
37	chr19:56091000-56092400	Active TSS	HUVEC	blood vessel
38	chr19:56091000-56092400	Active TSS	NH-A	brain
39	chr19:56091000-56092400	Active TSS	NHDF-Ad	bronchial
40	chr19:56091000-56092400	Active TSS	NHLF	lung
41	chr19:56091000-56092600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:56091000-56092600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:56091000-56092600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:56091000-56092600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr19:56091000-56092600	Active TSS	Gastric	stomach
46	chr19:56091000-56092600	Active TSS	Psoas Muscle	Psoas
47	chr19:56091000-56092600	Active TSS	Right Atrium	heart
48	chr19:56091000-56092800	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:56091000-56092800	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:56091000-56092800	Active TSS	iPS-20b Cell Line	embryonic stem cell

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