Variant report

Variant	rs11672854
Chromosome Location	chr19:52900846-52900847
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	ELF1	chr19:52900762-52901486	SK-N-SH	brain:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124
2	ELF1	chr19:52900846-52901409	MCF-7	breast:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124
3	RAD21	chr19:52900822-52901709	IMR90	lung:	n/a	n/a
4	POLR2A	chr19:52900799-52901467	GM12878	blood:	n/a	n/a
5	ELF1	chr19:52900837-52901788	GM12878	blood:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124 chr19:52901729-52901742
6	ELF1	chr19:52900834-52901267	HepG2	liver:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124
7	POLR2A	chr19:52900776-52901399	GM12891	blood:	n/a	n/a
8	GABPA	chr19:52900812-52901324	A549	lung:	n/a	n/a
9	GABPA	chr19:52900535-52901740	MCF-7	breast:	n/a	n/a
10	ETS1	chr19:52900825-52901304	GM12878	blood:	n/a	chr19:52901064-52901075 chr19:52901219-52901232 chr19:52901076-52901087 chr19:52901065-52901075
11	HEY1	chr19:52900826-52901293	HepG2	liver:	n/a	n/a
12	MYBL2	chr19:52900754-52901182	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:52900821-52901252	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:52900793-52901344	MCF10A-Er-Src	breast:	n/a	n/a
15	TBP	chr19:52900797-52901221	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr19:52900807-52901408	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:52900798-52901290	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:52900840-52901382	ProgFib	skin:	n/a	n/a
19	POLR2A	chr19:52900838-52901627	GM12878	blood:	n/a	n/a
20	MAX	chr19:52900824-52901358	SK-N-SH	brain:	n/a	n/a
21	PML	chr19:52900661-52901493	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:52900791-52901326	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr19:52900329-52901799	IMR90	lung:	n/a	n/a
24	MXI1	chr19:52900596-52902332	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr19:52900831-52901634	GM19193	blood:	n/a	n/a
26	POLR2A	chr19:52900816-52901292	GM12891	blood:	n/a	n/a
27	POLR2A	chr19:52900825-52901322	H1-hESC	embryonic stem cell:	n/a	n/a
28	GABPA	chr19:52900815-52901487	HL-60	blood:	n/a	n/a
29	POLR2A	chr19:52900752-52901437	SK-N-SH	brain:	n/a	n/a
30	ELF1	chr19:52900721-52901478	MCF-7	breast:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124
31	NRF1	chr19:52900624-52901742	SK-N-SH	brain:	n/a	n/a
32	GABPA	chr19:52900745-52901930	SK-N-SH	brain:	n/a	n/a
33	REST	chr19:52900741-52902049	H1-neurons	neurons:	n/a	chr19:52901216-52901226 chr19:52901249-52901262
34	BCLAF1	chr19:52900832-52901375	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:52900772-52901454	HUVEC	blood vessel:	n/a	n/a
36	EGR1	chr19:52900828-52901614	H1-hESC	embryonic stem cell:	n/a	chr19:52901096-52901120
37	POLR2A	chr19:52900799-52901749	HL-60	blood:	n/a	n/a
38	TAF1	chr19:52900823-52901318	SK-N-SH	brain:	n/a	n/a
39	ELF1	chr19:52900753-52901506	GM12878	blood:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124
40	POLR2A	chr19:52900844-52901425	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:52900201-52901639	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr19:52900826-52901301	MCF-7	breast:	n/a	n/a
43	POLR2A	chr19:52900798-52901559	HepG2	liver:	n/a	n/a
44	MTA3	chr19:52900699-52901711	GM12878	blood:	n/a	n/a
45	GABPA	chr19:52900807-52901279	A549	lung:	n/a	n/a
46	POLR2A	chr19:52900846-52901568	GM18505	blood:	n/a	n/a
47	TAF7	chr19:52900769-52901126	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr19:52900745-52901668	HL-60	blood:	n/a	n/a
49	POLR2A	chr19:52900750-52901528	H1-hESC	embryonic stem cell:	n/a	n/a
50	ELF1	chr19:52900788-52901429	SK-N-SH	brain:	n/a	chr19:52901111-52901124 chr19:52901064-52901073 chr19:52901062-52901073 chr19:52901114-52901123 chr19:52901062-52901073 chr19:52901063-52901072 chr19:52901113-52901124

No.	Distal block	Cell Line	Cell type
1	chr19:52839189..52842101-chr19:52900021..52902093,2	MCF-7	breast:
2	chr19:52893005..52896642-chr19:52900305..52903556,3	MCF-7	breast:
3	chr19:52899758..52902696-chr19:52903314..52905986,3	MCF-7	breast:
4	chr19:52894785..52896519-chr19:52899562..52901653,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-1	chr19:52900715-52900985	ENSG00000246015
2	lnc-ZNF83-1	chr19:52900715-52901010	ENSG00000246015
3	lnc-ZNF83-1	chr19:52900715-52901010	ENSG00000269834.1
4	lnc-ZNF83-1	chr19:52900715-52901010	NONHSAT067544
5	lnc-ZNF83-1	chr19:52900715-52901010	NONHSAT067545
6	lnc-ZNF83-1	chr19:52900715-52901010	NONHSAT067546
7	lnc-ZNF83-1	chr19:52900715-52901019	ENSG00000269834.1
8	lnc-ZNF83-1	chr19:52900715-52900922	ENSG00000269834.1

Variant related genes	Relation type
ZNF528	TF binding region
ENSG00000269834	Chromatin interaction
ENSG00000167555	Chromatin interaction
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10406795	0.82[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs11084158	0.82[EUR][1000 genomes]
rs11666879	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11670607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836094	0.89[EUR][1000 genomes]
rs2290747	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2560993	0.87[EUR][1000 genomes]
rs56778898	0.89[EUR][1000 genomes]
rs60807333	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11672854	ZNF534	cis	Skin Sun Exposed Lower leg	GTEx
rs11672854	ZNF534	cis	Thyroid	GTEx
rs11672854	ZNF534	cis	Adipose Subcutaneous	GTEx
rs11672854	ZNF534	cis	lung	GTEx
rs11672854	ZNF528	cis	Adipose Subcutaneous	GTEx
rs11672854	ZNF534	cis	Artery Tibial	GTEx
rs11672854	ZNF534	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52897600-52901000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
2	chr19:52898000-52902200	ZNF genes & repeats	Placenta	Placenta
3	chr19:52898000-52902800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:52898200-52903600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr19:52898600-52901000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
6	chr19:52899800-52901400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr19:52899800-52901400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr19:52899800-52901800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:52900000-52901600	Active TSS	Muscle Satellite Cultured Cells	--
10	chr19:52900000-52901600	Active TSS	Brain Cingulate Gyrus	brain
11	chr19:52900000-52901600	Active TSS	NHDF-Ad	bronchial
12	chr19:52900000-52902000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:52900000-52902000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:52900000-52902000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
15	chr19:52900000-52902000	Active TSS	NHLF	lung
16	chr19:52900200-52901000	Weak transcription	Spleen	Spleen
17	chr19:52900200-52901200	Active TSS	Brain Germinal Matrix	brain
18	chr19:52900200-52901200	Active TSS	HUVEC	blood vessel
19	chr19:52900200-52901400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:52900200-52901400	Active TSS	Fetal Lung	lung
21	chr19:52900200-52901400	Active TSS	Right Ventricle	heart
22	chr19:52900200-52901400	Active TSS	NHEK	skin
23	chr19:52900200-52901600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:52900200-52901600	Active TSS	Brain Hippocampus Middle	brain
25	chr19:52900200-52901600	Active TSS	Colonic Mucosa	Colon
26	chr19:52900200-52901600	Active TSS	Psoas Muscle	Psoas
27	chr19:52900200-52901800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr19:52900200-52901800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:52900200-52901800	Active TSS	Fetal Kidney	kidney
30	chr19:52900200-52901800	Active TSS	Ovary	ovary
31	chr19:52900200-52901800	ZNF genes & repeats	Thymus	Thymus
32	chr19:52900200-52902000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:52900200-52902000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr19:52900200-52902000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:52900200-52902000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:52900200-52902000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:52900200-52902200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr19:52900200-52902200	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr19:52900200-52902200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:52900200-52902200	ZNF genes & repeats	GM12878-XiMat	blood
41	chr19:52900200-52902200	Active TSS	HSMMtube	muscle
42	chr19:52900200-52902400	Active TSS	NH-A	brain
43	chr19:52900400-52901000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr19:52900400-52901000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr19:52900400-52901200	Weak transcription	Small Intestine	intestine
46	chr19:52900400-52901400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:52900400-52901400	Active TSS	Liver	Liver
48	chr19:52900400-52901400	Active TSS	Fetal Brain Female	brain
49	chr19:52900400-52901400	Active TSS	Fetal Muscle Trunk	muscle
50	chr19:52900400-52901400	Active TSS	Lung	lung

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