Variant report

Variant	rs11879347
Chromosome Location	chr19:56093556-56093557
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	ZBTB33	chr19:56092993-56093649	A549	lung:	n/a	n/a
2	GABPA	chr19:56091985-56093713	A549	lung:	n/a	n/a
3	FOSL2	chr19:56092074-56093868	A549	lung:	n/a	n/a
4	ETS1	chr19:56093111-56093640	A549	lung:	n/a	n/a
5	JUND	chr19:56092682-56093634	A549	lung:	n/a	n/a
6	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
7	NR3C1	chr19:56092770-56093869	A549	lung:	n/a	n/a
8	BCL3	chr19:56091329-56093788	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
9	BCL3	chr19:56092005-56093793	A549	lung:	n/a	chr19:56093661-56093670 chr19:56092350-56092359
10	TEAD4	chr19:56092622-56093618	A549	lung:	n/a	n/a
11	NR3C1	chr19:56092986-56093616	A549	lung:	n/a	n/a
12	REST	chr19:56092146-56093671	PANC-1	pancreas:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
13	NR3C1	chr19:56092996-56093765	A549	lung:	n/a	n/a
14	TCF7L2	chr19:56093360-56093625	PANC-1	pancreas:	n/a	n/a
15	ATF3	chr19:56093089-56093768	A549	lung:	n/a	n/a
16	MAX	chr19:56091376-56093828	A549	lung:	n/a	chr19:56092224-56092234 chr19:56091562-56091572 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
17	SIN3AK20	chr19:56092085-56093563	A549	lung:	n/a	n/a
18	FOXA1	chr19:56093022-56093799	A549	lung:	n/a	n/a
19	FOXA1	chr19:56093034-56093630	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:56093484-56093641	HUVEC	blood vessel:	n/a	n/a
21	MAFK	chr19:56092927-56093596	HepG2	liver:	n/a	n/a
22	GATA3	chr19:56092749-56093703	A549	lung:	n/a	n/a
23	EP300	chr19:56091976-56093855	A549	lung:	n/a	chr19:56093656-56093670
24	MAX	chr19:56091864-56093737	A549	lung:	n/a	chr19:56092224-56092234 chr19:56092600-56092610 chr19:56091909-56091919 chr19:56092361-56092371
25	FOXA2	chr19:56092587-56093710	A549	lung:	n/a	n/a
26	SRF	chr19:56093411-56093604	HepG2	liver:	n/a	n/a
27	GATA3	chr19:56091995-56093918	A549	lung:	n/a	n/a
28	NR3C1	chr19:56093098-56093720	A549	lung:	n/a	n/a
29	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
30	REST	chr19:56091942-56093753	A549	lung:	n/a	chr19:56092008-56092022 chr19:56092206-56092219 chr19:56092435-56092448
31	CUX1	chr19:56092265-56093561	K562	blood:	n/a	n/a
32	FOXA2	chr19:56093083-56093565	HepG2	liver:	n/a	n/a
33	TCF12	chr19:56091437-56093943	A549	lung:	n/a	n/a
34	REST	chr19:56091915-56093776	A549	lung:	n/a	chr19:56092008-56092022 chr19:56092206-56092219 chr19:56092435-56092448
35	USF1	chr19:56093148-56093791	A549	lung:	n/a	n/a
36	REST	chr19:56092102-56093644	PANC-1	pancreas:	n/a	chr19:56092206-56092219 chr19:56092435-56092448
37	TAL1	chr19:56093255-56093597	K562	blood:	n/a	n/a
38	ARID3A	chr19:56092852-56093681	HepG2	liver:	n/a	n/a
39	NR3C1	chr19:56093006-56093785	A549	lung:	n/a	n/a
40	FOSL2	chr19:56093254-56093571	A549	lung:	n/a	n/a
41	TEAD4	chr19:56093034-56093665	A549	lung:	n/a	n/a
42	TCF12	chr19:56093060-56093778	A549	lung:	n/a	n/a
43	GABPA	chr19:56092042-56093639	A549	lung:	n/a	n/a
44	USF1	chr19:56092063-56093635	A549	lung:	n/a	n/a
45	SIX5	chr19:56092008-56093781	A549	lung:	n/a	n/a
46	SIN3AK20	chr19:56092165-56093609	A549	lung:	n/a	n/a
47	ATF3	chr19:56092050-56093723	A549	lung:	n/a	n/a
48	CREB1	chr19:56093102-56093659	A549	lung:	n/a	n/a
49	NR3C1	chr19:56092795-56093907	A549	lung:	n/a	n/a
50	EP300	chr19:56093374-56093581	K562	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	chr19:56092829..56094744-chr19:56095214..56096826,2	MCF-7	breast:
8	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
9	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
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1079083	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]
rs1079084	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1079085	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11084402	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11665826	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11668725	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11668729	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11669682	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12610510	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs12610512	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610709	0.97[ASN][1000 genomes]
rs12610881	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972159	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12974617	0.95[ASN][1000 genomes]
rs12978375	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12979354	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12979366	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12980543	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2014329	0.87[ASN][1000 genomes]
rs2161456	0.82[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs2864433	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2902748	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34174244	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34715654	0.90[ASN][1000 genomes]
rs34937940	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35088354	0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs35197282	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35522245	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35839536	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs36047579	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60220392	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509945	0.82[JPT][hapmap]
rs71368855	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71368856	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246944	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7251733	0.99[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	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11879347	ZNF71	cis	parietal	SCAN
rs11879347	ZNF497	cis	parietal	SCAN
rs11879347	AURKC	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56092400-56093600	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr19:56092400-56093600	Flanking Active TSS	Fetal Intestine Large	intestine
3	chr19:56092400-56093800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:56092400-56093800	Flanking Active TSS	Liver	Liver
5	chr19:56092400-56094000	Flanking Active TSS	A549	lung
6	chr19:56092600-56093600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:56092600-56093600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:56092600-56096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:56092600-56097000	Weak transcription	Small Intestine	intestine
10	chr19:56092800-56093600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:56092800-56093600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:56092800-56093600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:56092800-56093600	Enhancers	Aorta	Aorta
14	chr19:56092800-56093600	Enhancers	Fetal Intestine Small	intestine
15	chr19:56092800-56093600	Enhancers	HMEC	breast
16	chr19:56092800-56093800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr19:56092800-56093800	Flanking Active TSS	Fetal Kidney	kidney
18	chr19:56092800-56094000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr19:56092800-56094000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr19:56092800-56094000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:56092800-56094000	Enhancers	Placenta	Placenta
22	chr19:56092800-56096200	Weak transcription	Right Ventricle	heart
23	chr19:56092800-56096600	Weak transcription	NH-A	brain
24	chr19:56092800-56096800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:56092800-56096800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:56092800-56096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:56092800-56096800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:56092800-56097000	Weak transcription	HSMMtube	muscle
29	chr19:56093000-56093600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:56093000-56093600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:56093000-56093600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:56093000-56093600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr19:56093000-56093600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:56093000-56093600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr19:56093000-56093600	Enhancers	Brain Angular Gyrus	brain
36	chr19:56093000-56093600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:56093000-56093600	Enhancers	Brain Substantia Nigra	brain
38	chr19:56093000-56093600	Enhancers	Colon Smooth Muscle	Colon
39	chr19:56093000-56093600	Enhancers	Fetal Lung	lung
40	chr19:56093000-56093600	Enhancers	Pancreas	Pancrea
41	chr19:56093000-56093600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr19:56093000-56093600	Enhancers	Hela-S3	cervix
43	chr19:56093000-56093800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr19:56093000-56093800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr19:56093000-56093800	Enhancers	Adipose Nuclei	Adipose
46	chr19:56093000-56094000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr19:56093000-56096800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:56093000-56096800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:56093000-56096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:56093000-56096800	Weak transcription	Fetal Brain Male	brain

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