Variant report

Variant	rs11671023
Chromosome Location	chr19:56154545-56154546
allele	A/C
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	RELA	chr19:56154313-56155140	GM19099	blood:	n/a	n/a
2	MAX	chr19:56151221-56155795	A549	lung:	n/a	chr19:56155426-56155435 chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56155425-56155436 chr19:56151538-56151549
3	POLR2A	chr19:56151273-56155759	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
5	BCL3	chr19:56154437-56155251	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:56154136-56155138	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:56153854-56155136	A549	lung:	n/a	n/a
8	POLR2A	chr19:56154042-56155145	GM12891	blood:	n/a	n/a
9	CHD1	chr19:56154386-56155215	IMR90	lung:	n/a	chr19:56154963-56154973
10	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
11	MAX	chr19:56153938-56155724	K562	blood:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
12	MYBL2	chr19:56154413-56155173	HepG2	liver:	n/a	n/a
13	SIN3AK20	chr19:56154481-56155266	SK-N-SH	brain:	n/a	n/a
14	GABPA	chr19:56154541-56155329	MCF-7	breast:	n/a	n/a
15	GATA3	chr19:56154034-56155247	A549	lung:	n/a	n/a
16	EGR1	chr19:56154109-56155347	HCT-116	colon:	n/a	chr19:56154853-56154863
17	E2F6	chr19:56154037-56155114	H1-hESC	embryonic stem cell:	n/a	chr19:56155023-56155033
18	MYC	chr19:56154176-56154570	MCF-7	breast:	n/a	n/a
19	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:56154041-56154729	HepG2	liver:	n/a	n/a
21	REST	chr19:56154533-56155318	A549	lung:	n/a	n/a
22	MAX	chr19:56153911-56155790	HepG2	liver:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
23	MAX	chr19:56154061-56155507	Hela-S3	cervix:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
24	POLR2A	chr19:56153839-56155319	A549	lung:	n/a	n/a
25	POLR2A	chr19:56153478-56155220	A549	lung:	n/a	n/a
26	POLR2A	chr19:56154253-56155152	K562	blood:	n/a	n/a
27	ELK1	chr19:56154274-56155110	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:56153442-56155799	K562	blood:	n/a	n/a
29	POLR2A	chr19:56153870-56155909	GM12892	blood:	n/a	n/a
30	ZBTB33	chr19:56154522-56155138	A549	lung:	n/a	n/a
31	POLR2A	chr19:56153525-56155261	MCF-7	breast:	n/a	n/a
32	FOXM1	chr19:56154423-56155141	GM12878	blood:	n/a	n/a
33	MAX	chr19:56154124-56155095	HUVEC	blood vessel:	n/a	n/a
34	HMGN3	chr19:56153824-56154548	K562	blood:	n/a	n/a
35	IRF1	chr19:56154454-56155079	K562	blood:	n/a	n/a
36	POLR2A	chr19:56154287-56155832	PFSK-1	brain:	n/a	n/a
37	CHD2	chr19:56151532-56155316	Hela-S3	cervix:	n/a	chr19:56154963-56154973 chr19:56152366-56152373
38	CUX1	chr19:56154486-56155043	GM12878	blood:	n/a	n/a
39	YY1	chr19:56154444-56155147	ECC-1	luminal epithelium:	n/a	chr19:56155025-56155034 chr19:56155067-56155076
40	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr19:56153491-56155368	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr19:56153814-56155640	HCT-116	colon:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
43	BCLAF1	chr19:56154525-56155132	GM12878	blood:	n/a	n/a
44	PAX5	chr19:56154185-56155109	GM12878	blood:	n/a	n/a
45	SIN3AK20	chr19:56154504-56155119	A549	lung:	n/a	n/a
46	TAF1	chr19:56154350-56155122	H1-hESC	embryonic stem cell:	n/a	n/a
47	ESRRA	chr19:56154205-56155663	GM12878	blood:	n/a	chr19:56155635-56155653
48	BCL3	chr19:56151732-56155150	A549	lung:	n/a	chr19:56153847-56153856 chr19:56152354-56152363 chr19:56152485-56152494
49	RELA	chr19:56154370-56155137	GM10847	blood:	n/a	n/a
50	MAX	chr19:56153939-56155716	MCF-7	breast:	n/a	chr19:56155426-56155435 chr19:56155425-56155436

No.	Distal block	Cell Line	Cell type
1	chr19:56107792..56111497-chr19:56151607..56154571,3	MCF-7	breast:
2	chr19:55894292..55897074-chr19:56152142..56154833,2	MCF-7	breast:
3	chr17:56708699..56709256-chr19:56154389..56155102,2	HCT-116	colon:
4	chr19:55996982..55998485-chr19:56153883..56155903,2	K562	blood:
5	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
6	chr19:55964915..55966958-chr19:56152410..56155336,2	K562	blood:
7	chr19:55628447..55630304-chr19:56152037..56154900,2	K562	blood:
8	chr19:56154222..56156750-chr19:56202512..56205168,2	K562	blood:
9	chr15:73075542..73076065-chr19:56154056..56155027,2	HCT-116	colon:
10	chr19:56110523..56113100-chr19:56152133..56154992,3	K562	blood:
11	chr19:56110029..56112023-chr19:56153492..56156368,2	K562	blood:
12	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
13	chr19:56154378..56155395-chr19:56164636..56165646,5	K562	blood:
14	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
15	chr19:55917778..55920684-chr19:56153894..56155704,2	K562	blood:
16	chr19:56153424..56156443-chr19:56220513..56224838,3	K562	blood:
17	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
18	chr19:55996765..55998431-chr19:56152633..56154883,2	MCF-7	breast:
19	chr19:55896816..55898587-chr19:56153997..56156129,2	MCF-7	breast:
20	chr1:245027711..245028675-chr19:56154452..56155229,2	Hela-S3	cervix:
21	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
22	chr19:55998666..56000299-chr19:56153756..56156154,2	K562	blood:
23	chr19:56152964..56155802-chr19:56186387..56188533,2	MCF-7	breast:

Variant related genes	Relation type
CCDC106	TF binding region
ZNF581	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000153187	Chromatin interaction
ENSG00000273175	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000269574	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000159322	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11084406	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665872	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666362	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882068	1.00[MEX][hapmap]
rs2112799	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786650	1.00[ASN][1000 genomes]
rs4541174	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801261	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs73062531	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062564	1.00[ASN][1000 genomes]
rs8104386	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11671023	CHMP2A	cis	parietal	SCAN
rs11671023	ZNF460	cis	parietal	SCAN
rs11671023	ZNF580	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56151600-56154800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr19:56151600-56155600	Active TSS	Ovary	ovary
3	chr19:56151600-56155800	Active TSS	Fetal Kidney	kidney
4	chr19:56151600-56156000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:56151600-56156200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:56151600-56156200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:56151800-56154800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:56151800-56155800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:56151800-56156000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:56151800-56156000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:56152000-56155800	Active TSS	H1 Cell Line	embryonic stem cell
15	chr19:56152200-56156000	Active TSS	Small Intestine	intestine
16	chr19:56152600-56154800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:56152600-56154800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr19:56152600-56155000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:56152600-56156000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:56152800-56154800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr19:56152800-56154800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:56152800-56154800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:56152800-56154800	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr19:56152800-56154800	Flanking Active TSS	Colonic Mucosa	Colon
25	chr19:56152800-56154800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr19:56152800-56154800	Flanking Active TSS	HUVEC	blood vessel
27	chr19:56152800-56155000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:56152800-56155000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:56152800-56155000	Flanking Active TSS	Liver	Liver
30	chr19:56152800-56155000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr19:56152800-56155000	Flanking Active TSS	Dnd41	blood
32	chr19:56152800-56155800	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr19:56152800-56156000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr19:56153000-56155000	Flanking Active TSS	Hela-S3	cervix
35	chr19:56153000-56155800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:56153200-56154600	Enhancers	Stomach Mucosa	stomach
37	chr19:56153400-56154800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr19:56153400-56154800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr19:56153400-56154800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:56153400-56154800	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr19:56153400-56155000	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr19:56153400-56155000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr19:56153600-56154600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr19:56153600-56154800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:56153600-56154800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:56153600-56154800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr19:56153600-56155000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:56153600-56155000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:56153600-56155000	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr19:56153600-56155000	Flanking Active TSS	HMEC	breast

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