Variant report

Variant	rs55801623
Chromosome Location	chr19:37019536-37019537
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:441)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:441 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr19:37019101-37020062	A549	lung:	n/a	n/a
2	CREB1	chr19:37019052-37019599	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr19:37018781-37019998	A549	lung:	n/a	chr19:37019562-37019584 chr19:37019614-37019628 chr19:37019565-37019573
4	POLR2A	chr19:37018795-37020195	GM12892	blood:	n/a	n/a
5	CHD2	chr19:37018938-37019880	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr19:37018932-37019906	K562	blood:	n/a	chr19:37019562-37019584 chr19:37019614-37019628 chr19:37019565-37019573
7	CHD2	chr19:37019000-37019969	Hela-S3	cervix:	n/a	n/a
8	ELF1	chr19:37018903-37019944	A549	lung:	n/a	n/a
9	POLR2A	chr19:37018919-37020220	Hela-S3	cervix:	n/a	n/a
10	RELA	chr19:37018840-37020359	GM19099	blood:	n/a	n/a
11	POLR2A	chr19:37018755-37019988	MCF-7	breast:	n/a	n/a
12	SMARCB1	chr19:37018795-37020100	Hela-S3	cervix:	n/a	chr19:37019596-37019605
13	MAFK	chr19:37019139-37019815	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr19:37018907-37019910	HepG2	liver:	n/a	n/a
15	TCF12	chr19:37018990-37019968	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr19:37018698-37020410	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:37018853-37019863	Gliobla	brain:	n/a	n/a
18	RCOR1	chr19:37018832-37020087	HepG2	liver:	n/a	n/a
19	USF2	chr19:37019353-37020234	GM12878	blood:	n/a	n/a
20	ZBTB33	chr19:37019020-37019944	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr19:37018624-37019887	K562	blood:	n/a	n/a
22	SIX5	chr19:37018993-37020083	A549	lung:	n/a	chr19:37019598-37019607 chr19:37019594-37019608 chr19:37019596-37019605
23	FOSL2	chr19:37018786-37019926	A549	lung:	n/a	n/a
24	ZBTB33	chr19:37019380-37019856	GM12878	blood:	n/a	n/a
25	USF2	chr19:37019381-37019915	HepG2	liver:	n/a	n/a
26	SIN3A	chr19:37018472-37020398	H1-hESC	embryonic stem cell:	n/a	chr19:37019675-37019684
27	POLR2A	chr19:37018844-37019866	IMR90	lung:	n/a	n/a
28	PML	chr19:37018720-37019966	GM12878	blood:	n/a	n/a
29	TAF1	chr19:37018811-37019838	H1-neurons	neurons:	n/a	n/a
30	ETS1	chr19:37018763-37020270	A549	lung:	n/a	chr19:37019594-37019607 chr19:37019595-37019608
31	HEY1	chr19:37018943-37019867	HepG2	liver:	n/a	chr19:37019615-37019630 chr19:37019547-37019562
32	USF1	chr19:37019508-37019875	SK-N-SH_RA	brain:	n/a	n/a
33	PML	chr19:37018859-37019586	K562	blood:	n/a	n/a
34	MAX	chr19:37019113-37019838	HepG2	liver:	n/a	n/a
35	TCF12	chr19:37018790-37020097	A549	lung:	n/a	n/a
36	TCF3	chr19:37019438-37019815	GM12878	blood:	n/a	n/a
37	EP300	chr19:37019064-37020211	K562	blood:	n/a	n/a
38	RAD21	chr19:37018930-37019886	H1-hESC	embryonic stem cell:	n/a	chr19:37018956-37018966
39	GATA3	chr19:37018559-37020324	A549	lung:	n/a	n/a
40	SIX5	chr19:37019116-37019724	GM12878	blood:	n/a	chr19:37019598-37019607 chr19:37019594-37019608 chr19:37019596-37019605
41	USF1	chr19:37019514-37019828	K562	blood:	n/a	n/a
42	REST	chr19:37018868-37020119	A549	lung:	n/a	chr19:37019672-37019686 chr19:37019651-37019664 chr19:37019674-37019684
43	BRCA1	chr19:37019186-37019984	H1-hESC	embryonic stem cell:	n/a	n/a
44	BACH1	chr19:37018803-37020374	H1-hESC	embryonic stem cell:	n/a	n/a
45	KAP1	chr19:37019061-37020181	U2OS	brain:	n/a	n/a
46	TAF1	chr19:37019222-37019851	Hela-S3	cervix:	n/a	n/a
47	FOS	chr19:37019009-37019915	HUVEC	blood vessel:	n/a	n/a
48	BRCA1	chr19:37018977-37019895	Hela-S3	cervix:	n/a	n/a
49	RELA	chr19:37018903-37020427	GM15510	blood:	n/a	n/a
50	MAX	chr19:37019017-37020003	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36978821..36980790-chr19:37017858..37020685,3	K562	blood:
2	chr19:37019103..37021335-chr19:37062459..37064743,4	K562	blood:
3	chr19:37017743..37019603-chr19:37263003..37264867,2	MCF-7	breast:
4	chr19:37014827..37016384-chr19:37017913..37020178,2	K562	blood:
5	chr19:36869703..36871321-chr19:37018127..37020542,2	K562	blood:
6	chr19:37018814..37019652-chr6:292056..292904,2	Hela-S3	cervix:
7	chr19:37018139..37019685-chr19:37156038..37157932,2	MCF-7	breast:
8	chr19:36979124..36982554-chr19:37017679..37020247,4	MCF-7	breast:
9	chr19:37019171..37020688-chr19:37117854..37120209,2	K562	blood:
10	chr12:92538963..92539741-chr19:37019212..37020041,2	Hela-S3	cervix:
11	chr19:36978148..36981795-chr19:37018105..37021194,8	K562	blood:
12	chr19:37017852..37021325-chr19:37033943..37038779,6	K562	blood:
13	chr11:46721841..46722466-chr19:37019388..37020036,2	Hela-S3	cervix:
14	chr19:37018711..37023188-chr19:37060299..37065354,5	K562	blood:
15	chr19:36868756..36870628-chr19:37018916..37021157,2	MCF-7	breast:
16	chr19:36628146..36630638-chr19:37017222..37019646,2	K562	blood:
17	chr19:37012845..37016384-chr19:37017166..37020287,4	K562	blood:
18	chr1:36234962..36235535-chr19:37019536..37020061,2	Hela-S3	cervix:
19	chr19:37017989..37021035-chr19:37064029..37066517,3	MCF-7	breast:
20	chr19:36979323..36981752-chr19:37018816..37021173,2	MCF-7	breast:
21	chr19:37017864..37019585-chr19:37067468..37069306,2	K562	blood:
22	chr19:36980411..36980990-chr19:37019063..37019816,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ZNF260	TF binding region
ENSG00000233527	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000245904	Chromatin interaction
ENSG00000142065	Chromatin interaction
ENSG00000092853	Chromatin interaction
ENSG00000267309	Chromatin interaction
ENSG00000197808	Chromatin interaction
ENSG00000266973	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000175213	Chromatin interaction
ENSG00000112679	Chromatin interaction
ENSG00000133639	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000266935	Chromatin interaction
ENSG00000175220	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs17707014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707021	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707033	0.87[ASN][1000 genomes]
rs2891868	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4514798	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4806328	0.86[AMR][1000 genomes]
rs4806333	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55634974	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55743839	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55830504	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880628	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55933007	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054915	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56075402	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56183102	0.84[AMR][1000 genomes]
rs56246998	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57126710	0.87[ASN][1000 genomes]
rs6510549	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7249099	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7257899	0.85[EUR][1000 genomes]
rs7259057	0.84[AMR][1000 genomes]
rs73032465	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73032484	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032489	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032491	0.87[ASN][1000 genomes]
rs73032502	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034106	0.87[ASN][1000 genomes]
rs73034109	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034142	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034176	0.88[EUR][1000 genomes]
rs73049817	0.86[AMR][1000 genomes]
rs73049826	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73049851	0.82[AMR][1000 genomes]
rs73049853	0.82[AMR][1000 genomes]
rs8100340	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8102097	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102474	0.87[ASN][1000 genomes]
rs8103917	0.82[AMR][1000 genomes]
rs8104893	0.86[AMR][1000 genomes]
rs8106144	0.87[ASN][1000 genomes]
rs8110140	0.84[AMR][1000 genomes]
rs8111192	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55801623	ZNF260	cis	Esophagus Mucosa	GTEx
rs55801623	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37017600-37020600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:37017600-37020600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:37017800-37019600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:37017800-37019800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:37017800-37019800	Active TSS	Fetal Kidney	kidney
6	chr19:37017800-37020000	Active TSS	Right Ventricle	heart
7	chr19:37017800-37020000	Active TSS	NHLF	lung
8	chr19:37017800-37020200	Active TSS	Fetal Muscle Trunk	muscle
9	chr19:37017800-37020600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:37017800-37020600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37018000-37019600	Active TSS	Colonic Mucosa	Colon
12	chr19:37018000-37019800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr19:37018000-37019800	Active TSS	Stomach Smooth Muscle	stomach
14	chr19:37018000-37019800	Active TSS	HMEC	breast
15	chr19:37018000-37020000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:37018000-37020000	Active TSS	NHDF-Ad	bronchial
17	chr19:37018000-37020400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:37018000-37020400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:37018000-37020400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:37018000-37020400	Active TSS	HSMM	muscle
21	chr19:37018000-37021000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:37018000-37021000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:37018000-37021000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:37018200-37019800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr19:37018200-37019800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:37018200-37019800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:37018200-37019800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:37018200-37019800	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr19:37018200-37019800	Active TSS	Duodenum Mucosa	Duodenum
30	chr19:37018200-37019800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr19:37018200-37019800	Active TSS	Fetal Stomach	stomach
32	chr19:37018200-37019800	Active TSS	Rectal Smooth Muscle	rectum
33	chr19:37018200-37019800	Active TSS	Hela-S3	cervix
34	chr19:37018200-37019800	Active TSS	NH-A	brain
35	chr19:37018200-37019800	Active TSS	NHEK	skin
36	chr19:37018200-37020000	Active TSS	Brain Germinal Matrix	brain
37	chr19:37018200-37020000	Active TSS	HSMMtube	muscle
38	chr19:37018200-37020000	Active TSS	K562	blood
39	chr19:37018200-37020200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr19:37018200-37020200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:37018200-37020200	Active TSS	Colon Smooth Muscle	Colon
42	chr19:37018200-37020200	Active TSS	Fetal Brain Female	brain
43	chr19:37018200-37020200	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr19:37018200-37020400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:37018200-37020400	Active TSS	H9 Cell Line	embryonic stem cell
46	chr19:37018200-37020400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:37018200-37020600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr19:37018200-37020600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:37018200-37020600	Active TSS	GM12878-XiMat	blood
50	chr19:37018200-37020800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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