Variant report

Variant	rs58997823
Chromosome Location	chr19:18398720-18398721
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	EP300	chr19:18398458-18399291	ECC-1	luminal epithelium:	n/a	chr19:18398992-18399008 chr19:18398910-18398924
2	ESR1	chr19:18398715-18399148	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3A	chr19:18398671-18399072	H1-hESC	embryonic stem cell:	n/a	n/a
4	RXRA	chr19:18398606-18399053	H1-hESC	embryonic stem cell:	n/a	chr19:18398936-18398943
5	TEAD4	chr19:18398609-18399104	H1-hESC	embryonic stem cell:	n/a	chr19:18398870-18398879
6	RAD21	chr19:18398647-18399164	ECC-1	luminal epithelium:	n/a	chr19:18399018-18399028 chr19:18399016-18399028
7	ESR1	chr19:18398670-18399071	ECC-1	luminal epithelium:	n/a	n/a
8	ESR1	chr19:18398692-18399073	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr19:18398646-18399181	ECC-1	luminal epithelium:	n/a	n/a
10	TAF1	chr19:18398599-18399118	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr19:18398695-18398976	H1-hESC	embryonic stem cell:	n/a	n/a
12	ATF2	chr19:18398551-18398949	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZBTB7A	chr19:18398375-18399393	ECC-1	luminal epithelium:	n/a	chr19:18398850-18398859
14	POLR2A	chr19:18398672-18399113	ECC-1	luminal epithelium:	n/a	n/a
15	TEAD4	chr19:18398571-18399218	ECC-1	luminal epithelium:	n/a	chr19:18398870-18398879
16	BACH1	chr19:18398664-18398985	H1-hESC	embryonic stem cell:	n/a	n/a
17	GABPA	chr19:18398659-18399051	H1-hESC	embryonic stem cell:	n/a	n/a
18	SP4	chr19:18398568-18399102	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF12	chr19:18398605-18399134	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:18397851-18399174	K562	blood:	n/a	n/a
21	TBP	chr19:18398708-18399171	H1-hESC	embryonic stem cell:	n/a	n/a
22	ATF2	chr19:18398596-18398975	H1-hESC	embryonic stem cell:	n/a	n/a
23	NR3C1	chr19:18398705-18399093	ECC-1	luminal epithelium:	n/a	chr19:18398960-18398973
24	NFIC	chr19:18398627-18399216	ECC-1	luminal epithelium:	n/a	n/a
25	SIN3AK20	chr19:18398713-18399070	H1-hESC	embryonic stem cell:	n/a	n/a
26	SP1	chr19:18398561-18399182	H1-hESC	embryonic stem cell:	n/a	chr19:18398714-18398728
27	JUND	chr19:18398611-18399183	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:18398581-18399180	SK-N-MC	brain:	n/a	n/a
29	TEAD4	chr19:18398579-18399202	ECC-1	luminal epithelium:	n/a	chr19:18398870-18398879
30	FOXM1	chr19:18398599-18399226	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr19:18398653-18399031	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTBP2	chr19:18398634-18399018	H1-hESC	embryonic stem cell:	n/a	n/a
33	TEAD4	chr19:18398601-18399137	H1-hESC	embryonic stem cell:	n/a	chr19:18398870-18398879
34	ESR1	chr19:18398675-18399026	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr19:18398586-18399166	ECC-1	luminal epithelium:	n/a	n/a
36	ZNF143	chr19:18398659-18399122	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr19:18398670-18399103	H1-hESC	embryonic stem cell:	n/a	chr19:18398992-18399008 chr19:18398910-18398924
38	ZBTB7A	chr19:18398704-18398928	HepG2	liver:	n/a	chr19:18398850-18398859
39	EP300	chr19:18398654-18399245	ECC-1	luminal epithelium:	n/a	chr19:18398992-18399008 chr19:18398910-18398924
40	ESR1	chr19:18398658-18399109	ECC-1	luminal epithelium:	n/a	n/a
41	ZBTB7A	chr19:18398636-18398865	K562	blood:	n/a	chr19:18398850-18398859
42	TCF12	chr19:18398449-18399412	ECC-1	luminal epithelium:	n/a	n/a
43	ZBTB7A	chr19:18398528-18399245	ECC-1	luminal epithelium:	n/a	chr19:18398850-18398859
44	TCF12	chr19:18398472-18399314	ECC-1	luminal epithelium:	n/a	n/a
45	SIX5	chr19:18398632-18399038	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18396145..18399548-chr19:18528063..18530226,4	K562	blood:
2	chr19:18397375..18399268-chr19:18401136..18404109,3	MCF-7	breast:
3	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
4	chr19:18397948..18402412-chr19:18484415..18487037,3	K562	blood:

Variant related genes	Relation type
RPL39P38	TF binding region
ENSG00000221167	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130511	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10419232	0.81[EUR][1000 genomes]
rs41446250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57734410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57934386	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59783649	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60235938	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73005418	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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 miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
7	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
9	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
10	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
12	esv1793726	chr19:18381600-18400786	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	104 gene(s)	inside rSNPs	diseases
13	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
14	nsv963018	chr19:18395612-18399311	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18393800-18399000	Weak transcription	Fetal Kidney	kidney
2	chr19:18393800-18401000	Weak transcription	Thymus	Thymus
3	chr19:18393800-18401200	Weak transcription	Right Atrium	heart
4	chr19:18393800-18402000	Weak transcription	Aorta	Aorta
5	chr19:18394000-18398800	Weak transcription	Fetal Lung	lung
6	chr19:18394000-18398800	Weak transcription	A549	lung
7	chr19:18394000-18400400	Weak transcription	Dnd41	blood
8	chr19:18394000-18400600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:18394000-18400800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:18394000-18401200	Weak transcription	Brain Hippocampus Middle	brain
11	chr19:18394000-18401400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:18394000-18401400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:18394000-18402000	Weak transcription	Brain Anterior Caudate	brain
14	chr19:18394000-18402800	Weak transcription	Gastric	stomach
15	chr19:18394400-18399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:18394400-18399000	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:18394400-18399200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:18394400-18400400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr19:18394400-18400600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:18394400-18400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:18394400-18401000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:18394400-18402000	Weak transcription	Pancreas	Pancrea
23	chr19:18394400-18402000	Weak transcription	Right Ventricle	heart
24	chr19:18394600-18400600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:18394600-18402200	Weak transcription	Psoas Muscle	Psoas
26	chr19:18395400-18399600	Enhancers	Fetal Muscle Leg	muscle
27	chr19:18395800-18400600	Weak transcription	Lung	lung
28	chr19:18395800-18400600	Weak transcription	Spleen	Spleen
29	chr19:18396000-18398800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:18396000-18400600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:18396000-18401000	Weak transcription	Colonic Mucosa	Colon
32	chr19:18396000-18402600	Weak transcription	Small Intestine	intestine
33	chr19:18396200-18398800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:18396200-18401000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:18396200-18402600	Weak transcription	Liver	Liver
36	chr19:18396400-18398800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:18396400-18398800	Weak transcription	Fetal Heart	heart
38	chr19:18396400-18399000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:18396400-18399000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:18396400-18399200	Weak transcription	Primary B cells from cord blood	blood
41	chr19:18396400-18399200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:18396400-18399400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:18396400-18400000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr19:18396400-18400200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:18396400-18400400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:18396400-18400400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:18396400-18400600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:18396400-18400800	Weak transcription	Adipose Nuclei	Adipose
49	chr19:18396400-18401400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:18396600-18399000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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