Variant report

Variant	rs7260466
Chromosome Location	chr19:39420802-39420803
allele	C/T
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	chr19:39420661-39422148	A549	lung:	n/a	n/a
2	MXI1	chr19:39420724-39422170	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39420743-39421919	U87	brain:	n/a	n/a
4	NRF1	chr19:39420611-39422157	SK-N-SH	brain:	n/a	chr19:39421093-39421107 chr19:39421090-39421104 chr19:39421073-39421084 chr19:39421092-39421103 chr19:39421093-39421104
5	YY1	chr19:39420699-39421723	ECC-1	luminal epithelium:	n/a	chr19:39421087-39421101
6	GABPA	chr19:39420693-39422203	A549	lung:	n/a	chr19:39421093-39421107 chr19:39421090-39421104 chr19:39421093-39421104
7	TEAD4	chr19:39420548-39422095	K562	blood:	n/a	n/a
8	CTCF	chr19:39420756-39421294	K562	blood:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
9	MAX	chr19:39420755-39421949	SK-N-SH	brain:	n/a	n/a
10	STAT1	chr19:39420743-39421762	GM12878	blood:	n/a	chr19:39421007-39421015 chr19:39420788-39420800
11	TEAD4	chr19:39420661-39421394	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZNF263	chr19:39420732-39421966	HEK293-T-REx	kidney:	n/a	n/a
13	RUNX3	chr19:39420565-39422173	GM12878	blood:	n/a	chr19:39420776-39420785
14	MAX	chr19:39420672-39421788	K562	blood:	n/a	n/a
15	CHD2	chr19:39420795-39421795	H1-hESC	embryonic stem cell:	n/a	n/a
16	CREB1	chr19:39420643-39421891	HepG2	liver:	n/a	n/a
17	MYC	chr19:39420783-39421830	NB4	blood:	n/a	n/a
18	TAF1	chr19:39420621-39421997	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr19:39419973-39422967	A549	lung:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
20	MYC	chr19:39420797-39421871	Hela-S3	cervix:	n/a	n/a
21	TEAD4	chr19:39420578-39421291	A549	lung:	n/a	n/a
22	ZNF143	chr19:39420791-39421830	H1-hESC	embryonic stem cell:	n/a	chr19:39421090-39421100
23	CEBPB	chr19:39420790-39421206	K562	blood:	n/a	n/a
24	CTCF	chr19:39420734-39421544	MCF-7	breast:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
25	CTCF	chr19:39420772-39421259	SK-N-SH_RA	brain:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
26	CTCF	chr19:39420786-39421401	HepG2	liver:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
27	POLR2A	chr19:39420786-39422005	MCF10A-Er-Src	breast:	n/a	n/a
28	SIN3AK20	chr19:39420531-39422245	MCF-7	breast:	n/a	n/a
29	SIN3AK20	chr19:39420376-39422495	A549	lung:	n/a	n/a
30	CTCF	chr19:39420176-39422260	SK-N-SH	brain:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
31	TCF12	chr19:39420763-39421813	ECC-1	luminal epithelium:	n/a	n/a
32	RAD21	chr19:39420641-39421383	A549	lung:	n/a	chr19:39421087-39421101
33	MXI1	chr19:39420660-39422526	SK-N-SH	brain:	n/a	n/a
34	CTCF	chr19:39420651-39421468	A549	lung:	n/a	chr19:39421022-39421040 chr19:39421023-39421039
35	YY1	chr19:39420583-39421614	H1-hESC	embryonic stem cell:	n/a	chr19:39421087-39421101
36	CHD1	chr19:39420736-39422193	GM12878	blood:	n/a	n/a
37	CREB1	chr19:39420579-39421861	K562	blood:	n/a	n/a
38	CEBPB	chr19:39420589-39421494	GM12878	blood:	n/a	chr19:39421459-39421467
39	RUNX3	chr19:39420595-39422425	GM12878	blood:	n/a	chr19:39420776-39420785
40	SIX5	chr19:39420717-39422000	A549	lung:	n/a	n/a
41	RAD21	chr19:39420755-39421244	ECC-1	luminal epithelium:	n/a	chr19:39421087-39421101
42	TAF1	chr19:39420721-39422107	A549	lung:	n/a	n/a
43	NR2F2	chr19:39420677-39422057	K562	blood:	n/a	n/a
44	POLR2A	chr19:39420749-39422156	PFSK-1	brain:	n/a	n/a
45	TEAD4	chr19:39420721-39421284	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:39420786-39421870	H1-neurons	neurons:	n/a	n/a
47	SMC3	chr19:39420737-39421396	GM12878	blood:	n/a	chr19:39421024-39421038
48	ZKSCAN1	chr19:39420383-39421869	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr19:39420685-39421985	U87	brain:	n/a	n/a
50	TEAD4	chr19:39420666-39421528	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39420462..39423214-chr19:39898290..39900735,2	K562	blood:
2	chr19:39336974..39342883-chr19:39419267..39423173,13	K562	blood:
3	chr19:39398838..39403067-chr19:39419638..39422578,4	MCF-7	breast:
4	chr19:39338595..39344864-chr19:39418604..39422934,11	K562	blood:
5	chr19:39360175..39362471-chr19:39419567..39421419,2	MCF-7	breast:
6	chr19:39322407..39324148-chr19:39419876..39421918,2	K562	blood:
7	chr19:39226181..39228990-chr19:39419347..39420876,2	K562	blood:
8	chr19:39386472..39392494-chr19:39418718..39424791,9	K562	blood:
9	chr19:39326367..39329872-chr19:39419342..39422625,3	MCF-7	breast:
10	chr19:39388885..39392214-chr19:39419332..39422757,5	MCF-7	breast:
11	chr19:39358835..39360669-chr19:39419879..39421985,2	K562	blood:
12	chr19:39411897..39413585-chr19:39419804..39422534,2	K562	blood:
13	chr19:39401097..39402936-chr19:39418975..39421481,2	K562	blood:
14	chr19:39420323..39422094-chr19:39898290..39901814,3	K562	blood:
15	chr19:39338960..39343184-chr19:39419440..39422855,6	MCF-7	breast:
16	chr19:39338909..39344654-chr19:39419169..39426961,19	MCF-7	breast:
17	chr19:39260065..39260751-chr19:39420671..39421390,2	MCF-7	breast:
18	chr19:39420306..39422739-chr19:39440304..39443002,2	K562	blood:
19	chr19:39226859..39228990-chr19:39419347..39420977,2	K562	blood:
20	chr19:39339391..39340580-chr19:39420505..39421476,3	MCF-7	breast:
21	chr19:39406282..39408716-chr19:39419182..39421050,3	K562	blood:
22	chr19:39411214..39414705-chr19:39419221..39421908,4	MCF-7	breast:
23	chr19:39370268..39372714-chr19:39419858..39422598,3	K562	blood:

Variant related genes	Relation type
MRPS12	TF binding region
SARS2	TF binding region
ENSG00000269190	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000262484	Chromatin interaction
ENSG00000269547	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000104835	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11544093	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459104	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12459197	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12459474	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12462338	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3181070	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247506	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733083	0.83[ASN][1000 genomes]
rs8108375	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39419800-39421000	Flanking Active TSS	Hela-S3	cervix
2	chr19:39420000-39421000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:39420000-39421000	Flanking Active TSS	Dnd41	blood
4	chr19:39420000-39422600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:39420200-39421000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:39420200-39421000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:39420200-39421000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:39420200-39421000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:39420200-39421000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:39420200-39421000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr19:39420200-39421000	Flanking Active TSS	HUVEC	blood vessel
12	chr19:39420200-39422400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:39420200-39422600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr19:39420200-39422600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:39420200-39422600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:39420200-39422600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr19:39420200-39422600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr19:39420400-39421000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr19:39420400-39421000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:39420400-39421000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:39420400-39421000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr19:39420400-39421000	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr19:39420400-39421000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr19:39420400-39421000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr19:39420400-39421000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr19:39420400-39421000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:39420400-39421000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr19:39420400-39421000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr19:39420400-39421000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr19:39420400-39421000	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr19:39420400-39421000	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr19:39420400-39421000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr19:39420400-39421000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr19:39420400-39421000	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr19:39420400-39421000	Flanking Active TSS	Fetal Thymus	thymus
36	chr19:39420400-39421000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr19:39420400-39421000	Flanking Active TSS	Thymus	Thymus
38	chr19:39420400-39421000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr19:39420400-39421000	Flanking Active TSS	NH-A	brain
40	chr19:39420400-39421000	Flanking Active TSS	NHDF-Ad	bronchial
41	chr19:39420400-39421000	Flanking Active TSS	NHLF	lung
42	chr19:39420400-39421000	Flanking Active TSS	Osteobl	bone
43	chr19:39420400-39421200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr19:39420400-39422400	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr19:39420400-39422400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr19:39420400-39422600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr19:39420400-39422600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:39420400-39422600	Active TSS	HSMM	muscle
49	chr19:39420400-39422600	Active TSS	HSMMtube	muscle
50	chr19:39420400-39422600	Active TSS	K562	blood

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