Variant report

Variant	rs2161456
Chromosome Location	chr19:56116915-56116916
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	NRF1	chr19:56116591-56117052	GM12878	blood:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116788-56116799 chr19:56116690-56116699 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116948-56116955
2	TAF1	chr19:56116145-56117446	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr19:56116736-56117037	HCT-116	colon:	n/a	n/a
4	STAT3	chr19:56116564-56116917	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr19:56115872-56117235	K562	blood:	n/a	chr19:56116532-56116542 chr19:56116876-56116886 chr19:56116995-56117005
6	RCOR1	chr19:56116350-56116969	HepG2	liver:	n/a	n/a
7	ELF1	chr19:56116562-56117239	MCF-7	breast:	n/a	chr19:56116946-56116955
8	IRF1	chr19:56115939-56117029	K562	blood:	n/a	chr19:56116533-56116547 chr19:56116689-56116703 chr19:56116513-56116527 chr19:56115982-56115996
9	MAX	chr19:56116159-56116991	A549	lung:	n/a	chr19:56116532-56116542 chr19:56116876-56116886
10	CHD2	chr19:56116064-56117353	Hela-S3	cervix:	n/a	chr19:56116997-56117007
11	SMC3	chr19:56116237-56116936	Hela-S3	cervix:	n/a	chr19:56116687-56116697 chr19:56116880-56116888 chr19:56116877-56116887
12	SP1	chr19:56115773-56118030	A549	lung:	n/a	chr19:56116015-56116025 chr19:56116530-56116544 chr19:56117056-56117070 chr19:56115982-56115994 chr19:56117707-56117714 chr19:56116691-56116700 chr19:56116998-56117007 chr19:56116533-56116545 chr19:56116515-56116524 chr19:56116997-56117009 chr19:56116015-56116025 chr19:56116690-56116700 chr19:56115982-56115994 chr19:56116689-56116701 chr19:56116691-56116700 chr19:56116515-56116524 chr19:56116513-56116525 chr19:56116690-56116699 chr19:56116514-56116524 chr19:56116670-56116680 chr19:56116535-56116544 chr19:56116533-56116545 chr19:56116686-56116700 chr19:56116670-56116680 chr19:56116534-56116544 chr19:56116997-56117009 chr19:56116690-56116700 chr19:56116689-56116701 chr19:56116535-56116544 chr19:56115984-56115993 chr19:56116514-56116524 chr19:56116514-56116523 chr19:56116991-56117000 chr19:56116994-56117008 chr19:56116513-56116525 chr19:56116534-56116544 chr19:56117444-56117453 chr19:56115979-56115993 chr19:56116510-56116524 chr19:56116534-56116543
13	MYC	chr19:56116882-56116971	HepG2	liver:	n/a	n/a
14	MAX	chr19:56116176-56117087	MCF-7	breast:	n/a	chr19:56116532-56116542 chr19:56116876-56116886 chr19:56116995-56117005
15	TCF7L2	chr19:56116234-56116916	Hela-S3	cervix:	n/a	n/a
16	HEY1	chr19:56116171-56116950	K562	blood:	n/a	n/a
17	POLR2A	chr19:56116230-56116951	HepG2	liver:	n/a	n/a
18	NRF1	chr19:56115804-56117411	SK-N-SH	brain:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116788-56116799 chr19:56116690-56116699 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116534-56116543 chr19:56116948-56116955
19	SP1	chr19:56115878-56117128	A549	lung:	n/a	chr19:56116015-56116025 chr19:56116530-56116544 chr19:56117056-56117070 chr19:56115982-56115994 chr19:56116691-56116700 chr19:56116998-56117007 chr19:56116533-56116545 chr19:56116515-56116524 chr19:56116997-56117009 chr19:56116015-56116025 chr19:56116690-56116700 chr19:56115982-56115994 chr19:56116689-56116701 chr19:56116691-56116700 chr19:56116515-56116524 chr19:56116513-56116525 chr19:56116690-56116699 chr19:56116514-56116524 chr19:56116670-56116680 chr19:56116535-56116544 chr19:56116533-56116545 chr19:56116686-56116700 chr19:56116670-56116680 chr19:56116534-56116544 chr19:56116997-56117009 chr19:56116690-56116700 chr19:56116689-56116701 chr19:56116535-56116544 chr19:56115984-56115993 chr19:56116514-56116524 chr19:56116514-56116523 chr19:56116991-56117000 chr19:56116994-56117008 chr19:56116513-56116525 chr19:56116534-56116544 chr19:56115979-56115993 chr19:56116510-56116524 chr19:56116534-56116543
20	YY1	chr19:56116549-56117313	HepG2	liver:	n/a	chr19:56117286-56117308 chr19:56116690-56116699 chr19:56117046-56117060
21	POLR2A	chr19:56115967-56117792	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr19:56116140-56117658	MCF-7	breast:	n/a	n/a
23	MAX	chr19:56115857-56118135	A549	lung:	n/a	chr19:56116532-56116542 chr19:56116876-56116886 chr19:56116995-56117005
24	GABPA	chr19:56116719-56117128	H1-hESC	embryonic stem cell:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116948-56116955
25	MAZ	chr19:56115892-56118114	K562	blood:	n/a	chr19:56116532-56116542 chr19:56116876-56116886 chr19:56116995-56117005
26	CREB1	chr19:56116566-56116994	A549	lung:	n/a	n/a
27	POLR2A	chr19:56115859-56118733	MCF10A-Er-Src	breast:	n/a	n/a
28	THAP1	chr19:56116614-56116945	K562	blood:	n/a	n/a
29	HDAC2	chr19:56116525-56116965	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:56116103-56117336	ProgFib	skin:	n/a	n/a
31	POLR2A	chr19:56116072-56117287	ECC-1	luminal epithelium:	n/a	n/a
32	SIN3AK20	chr19:56116527-56117020	SK-N-SH	brain:	n/a	n/a
33	ETS1	chr19:56115923-56117142	A549	lung:	n/a	chr19:56117011-56117024 chr19:56116688-56116699 chr19:56117012-56117021 chr19:56117012-56117021 chr19:56117010-56117021 chr19:56116945-56116954 chr19:56116734-56116743 chr19:56117012-56117021 chr19:56117012-56117021 chr19:56117009-56117025 chr19:56116039-56116050 chr19:56117012-56117021 chr19:56117012-56117021 chr19:56116532-56116543 chr19:56117012-56117021 chr19:56117010-56117020
34	GABPA	chr19:56115948-56117988	A549	lung:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116690-56116699 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116534-56116543 chr19:56116948-56116955
35	POLR2A	chr19:56115877-56117080	HCT-116	colon:	n/a	n/a
36	ELF1	chr19:56116540-56117117	SK-N-SH	brain:	n/a	chr19:56116946-56116955
37	ELF1	chr19:56116175-56118096	GM12878	blood:	n/a	chr19:56116946-56116955 chr19:56117777-56117789
38	ELF1	chr19:56116500-56117113	A549	lung:	n/a	chr19:56116946-56116955
39	PBX3	chr19:56115937-56117349	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr19:56115980-56117993	GM18505	blood:	n/a	n/a
41	POLR2A	chr19:56116562-56117234	K562	blood:	n/a	n/a
42	GABPA	chr19:56116713-56117120	HL-60	blood:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116948-56116955
43	POLR2A	chr19:56115798-56117257	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr19:56116060-56118071	IMR90	lung:	n/a	n/a
45	GABPA	chr19:56116552-56117202	HL-60	blood:	n/a	chr19:56116858-56116872 chr19:56116788-56116799 chr19:56116690-56116699 chr19:56116861-56116870 chr19:56116861-56116872 chr19:56116788-56116802 chr19:56116948-56116955
46	POLR2A	chr19:56115902-56117498	HL-60	blood:	n/a	n/a
47	POLR2A	chr19:56115858-56117932	HUVEC	blood vessel:	n/a	n/a
48	STAT1	chr19:56116273-56117293	GM12878	blood:	n/a	chr19:56116992-56117004
49	YY1	chr19:56116744-56117481	GM12892	blood:	n/a	chr19:56117286-56117308 chr19:56117046-56117060
50	RFX5	chr19:56115868-56118564	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56027948..56029107-chr19:56116801..56118236,12	K562	blood:
2	chr19:55917805..55920377-chr19:56116633..56119121,2	K562	blood:
3	chr19:55850159..55852267-chr19:56116484..56118952,2	MCF-7	breast:
4	chr19:56116757..56118714-chr19:56164640..56166848,2	MCF-7	breast:
5	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
6	chr19:56114907..56116947-chr19:56184542..56187154,2	K562	blood:
7	chr19:56115993..56118637-chr19:56165089..56166891,2	K562	blood:
8	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
9	chr19:56116914..56119642-chr19:56129157..56131500,3	K562	blood:
10	chr19:56089635..56093860-chr19:56114549..56117863,7	MCF-7	breast:
11	chr19:55971554..55973969-chr19:56116219..56118997,2	MCF-7	breast:
12	chr19:55987823..55989523-chr19:56114913..56117449,2	MCF-7	breast:
13	chr18:12883825..12884548-chr19:56116434..56117103,2	Hela-S3	cervix:
14	chr19:56114376..56117189-chr19:56151962..56154337,3	K562	blood:
15	chr19:56116188..56118514-chr19:56134480..56137487,3	MCF-7	breast:
16	chr19:56116639..56119326-chr19:56146420..56148377,2	K562	blood:

Variant related genes	Relation type
FIZ1	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000173581	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10451452	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1079082	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1079083	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs1079084	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11084402	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11879347	0.82[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]
rs12610510	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs34715654	0.85[AMR][1000 genomes]
rs35088354	0.87[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][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	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
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2161456	ZNF304	cis	parietal	SCAN
rs2161456	FAM46A	trans	lymphoblastoid	seeQTL
rs2161456	AURKC	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56115000-56117800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:56115400-56117800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:56115600-56117400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:56115600-56117600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:56115600-56117800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:56115600-56117800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:56115800-56117400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:56115800-56117400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:56115800-56117400	Active TSS	Fetal Brain Female	brain
10	chr19:56115800-56117800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:56115800-56117800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:56115800-56117800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:56115800-56117800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:56115800-56117800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:56115800-56117800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:56115800-56117800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:56115800-56117800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:56115800-56118000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr19:56115800-56118000	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:56116000-56117400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:56116000-56117600	Active TSS	Ovary	ovary
22	chr19:56116000-56117800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr19:56116000-56117800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:56116000-56117800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr19:56116000-56117800	Active TSS	Colon Smooth Muscle	Colon
26	chr19:56116000-56117800	Active TSS	Fetal Kidney	kidney
27	chr19:56116000-56117800	Active TSS	Psoas Muscle	Psoas
28	chr19:56116000-56117800	Active TSS	HSMMtube	muscle
29	chr19:56116000-56117800	Active TSS	K562	blood
30	chr19:56116000-56117800	Active TSS	NHDF-Ad	bronchial
31	chr19:56116000-56117800	Active TSS	NHLF	lung
32	chr19:56116000-56118000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:56116000-56118000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr19:56116000-56118200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:56116000-56118200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr19:56116000-56118200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:56116200-56117400	Active TSS	Placenta Amnion	Placenta Amnion
38	chr19:56116200-56117600	Active TSS	Brain Cingulate Gyrus	brain
39	chr19:56116200-56117600	Active TSS	Small Intestine	intestine
40	chr19:56116200-56117800	Active TSS	Left Ventricle	heart
41	chr19:56116200-56117800	Active TSS	Pancreas	Pancrea
42	chr19:56116200-56117800	Active TSS	Right Ventricle	heart
43	chr19:56116200-56117800	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr19:56116400-56117200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:56116400-56117200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:56116400-56117200	Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr19:56116400-56117200	Active TSS	Primary T cells from cord blood	blood
48	chr19:56116400-56117200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:56116400-56117200	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:56116400-56117200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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