Variant report

Variant	rs1079083
Chromosome Location	chr19:56092719-56092720
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	REST	chr19:56092103-56093468	PFSK-1	brain:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
2	REST	chr19:56092672-56093104	U87	brain:	n/a	n/a
3	GABPA	chr19:56091985-56093713	A549	lung:	n/a	n/a
4	FOSL2	chr19:56092074-56093868	A549	lung:	n/a	n/a
5	ZNF143	chr19:56092178-56093032	K562	blood:	n/a	chr19:56092241-56092259
6	GABPA	chr19:56092042-56092778	HL-60	blood:	n/a	n/a
7	JUND	chr19:56092143-56092998	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:56091707-56092814	MCF10A-Er-Src	breast:	n/a	n/a
9	REST	chr19:56092062-56093388	ECC-1	luminal epithelium:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
10	JUND	chr19:56092682-56093634	A549	lung:	n/a	n/a
11	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
12	RCOR1	chr19:56092045-56093086	K562	blood:	n/a	n/a
13	MAZ	chr19:56091119-56093072	IMR90	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
14	POLR2A	chr19:56091898-56092977	HUVEC	blood vessel:	n/a	n/a
15	MAZ	chr19:56091251-56092828	GM12878	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
16	MAZ	chr19:56091415-56093026	K562	blood:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
17	ZNF143	chr19:56092707-56093089	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXA1	chr19:56092633-56092991	T-47D	breast:	n/a	n/a
19	REST	chr19:56092707-56093097	GM12878	blood:	n/a	n/a
20	FOXA1	chr19:56092675-56093426	HepG2	liver:	n/a	n/a
21	HCFC1	chr19:56092126-56092973	K562	blood:	n/a	n/a
22	SIN3A	chr19:56091344-56093085	H1-hESC	embryonic stem cell:	n/a	n/a
23	BCL3	chr19:56091329-56093788	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
24	POLR2A	chr19:56091364-56092750	A549	lung:	n/a	n/a
25	REST	chr19:56092150-56093323	HCT-116	colon:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
26	BCL3	chr19:56092005-56093793	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
27	POLR2A	chr19:56091963-56093050	PANC-1	pancreas:	n/a	n/a
28	RCOR1	chr19:56092123-56093004	Hela-S3	cervix:	n/a	n/a
29	GABPA	chr19:56091861-56093159	K562	blood:	n/a	n/a
30	TEAD4	chr19:56092622-56093618	A549	lung:	n/a	n/a
31	POLR2A	chr19:56091640-56092882	HepG2	liver:	n/a	n/a
32	REST	chr19:56092710-56093104	U87	brain:	n/a	n/a
33	POLR2A	chr19:56091967-56093009	PANC-1	pancreas:	n/a	n/a
34	REST	chr19:56091979-56093313	PANC-1	pancreas:	n/a	chr19:56092008-56092022 chr19:56092206-56092219 chr19:56092435-56092448
35	MYBL2	chr19:56092171-56093002	HepG2	liver:	n/a	n/a
36	REST	chr19:56092089-56093464	ECC-1	luminal epithelium:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
37	REST	chr19:56092146-56093671	PANC-1	pancreas:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
38	MAX	chr19:56091376-56093828	A549	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
39	SIN3AK20	chr19:56092085-56093563	A549	lung:	n/a	n/a
40	REST	chr19:56092047-56093331	PANC-1	pancreas:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
41	GTF2F1	chr19:56092138-56092812	Hela-S3	cervix:	n/a	n/a
42	SIN3AK20	chr19:56092715-56092972	H1-hESC	embryonic stem cell:	n/a	n/a
43	IRF1	chr19:56092155-56093062	K562	blood:	n/a	n/a
44	GABPA	chr19:56091984-56092813	MCF-7	breast:	n/a	n/a
45	ZBTB7A	chr19:56091367-56092783	ECC-1	luminal epithelium:	n/a	n/a
46	REST	chr19:56092197-56093177	H1-hESC	embryonic stem cell:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
47	CHD1	chr19:56091005-56092989	IMR90	lung:	n/a	n/a
48	REST	chr19:56092054-56093507	HL-60	blood:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
49	TAF1	chr19:56091876-56092772	A549	lung:	n/a	n/a
50	POLR2A	chr19:56091977-56093078	Raji	blood:	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	chr19:56092293..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
ZNF579	TF binding region
ENSG00000267730	TF binding region
ENSG00000171443	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000261221	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10403462	0.84[ASN][1000 genomes]
rs10451452	0.82[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1079082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11665826	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668725	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668729	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669682	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879347	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12610510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610512	0.93[ASN][1000 genomes]
rs12610709	0.95[ASN][1000 genomes]
rs12610881	0.97[ASN][1000 genomes]
rs12972159	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974617	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12978375	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12979354	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12979366	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12980543	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014329	0.87[ASN][1000 genomes]
rs2161456	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2864433	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902748	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34174244	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34715654	0.87[ASN][1000 genomes]
rs34937940	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35088354	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs35197282	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35522245	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35839536	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36047579	0.91[ASN][1000 genomes]
rs60220392	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6509945	0.82[JPT][hapmap]
rs71368855	0.93[ASN][1000 genomes]
rs71368856	0.93[ASN][1000 genomes]
rs7246944	0.91[ASN][1000 genomes]
rs7251733	0.96[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1079083	ZNF71	cis	parietal	SCAN
rs1079083	ZNF497	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:56090800-56092800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:56091000-56092800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:56091000-56092800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:56091000-56092800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:56091000-56092800	Active TSS	Fetal Kidney	kidney
8	chr19:56091000-56092800	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:56091000-56092800	Active TSS	HSMMtube	muscle
10	chr19:56091000-56093000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:56091000-56093200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:56091000-56093200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:56091200-56092800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:56091200-56092800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:56091200-56092800	Active TSS	Esophagus	oesophagus
16	chr19:56091200-56092800	Active TSS	Lung	lung
17	chr19:56091200-56092800	Active TSS	Ovary	ovary
18	chr19:56091400-56092800	Active TSS	Aorta	Aorta
19	chr19:56091400-56092800	Active TSS	Right Ventricle	heart
20	chr19:56091400-56093000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:56091400-56093000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr19:56091400-56093000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:56091800-56092800	Active TSS	Brain Substantia Nigra	brain
24	chr19:56092200-56092800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr19:56092200-56092800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:56092400-56092800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr19:56092400-56092800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:56092400-56092800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:56092400-56092800	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr19:56092400-56092800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr19:56092400-56092800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:56092400-56092800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr19:56092400-56092800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:56092400-56092800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:56092400-56092800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:56092400-56092800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:56092400-56092800	Flanking Active TSS	Colonic Mucosa	Colon
38	chr19:56092400-56092800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr19:56092400-56092800	Flanking Active TSS	Fetal Brain Male	brain
40	chr19:56092400-56092800	Flanking Active TSS	Fetal Heart	heart
41	chr19:56092400-56092800	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr19:56092400-56092800	Flanking Active TSS	Fetal Muscle Trunk	muscle
43	chr19:56092400-56092800	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr19:56092400-56092800	Flanking Active TSS	Placenta	Placenta
45	chr19:56092400-56092800	Flanking Active TSS	Fetal Thymus	thymus
46	chr19:56092400-56092800	Flanking Active TSS	Left Ventricle	heart
47	chr19:56092400-56092800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr19:56092400-56092800	Flanking Active TSS	HMEC	breast
49	chr19:56092400-56092800	Flanking Active TSS	HUVEC	blood vessel
50	chr19:56092400-56092800	Flanking Active TSS	NH-A	brain

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