Variant report

Variant	rs3848623
Chromosome Location	chr19:39522891-39522892
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	NRF1	chr19:39521963-39523086	SK-N-SH	brain:	n/a	chr19:39522088-39522097
2	MAX	chr19:39521716-39522972	ECC-1	luminal epithelium:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
3	MAX	chr19:39521799-39522928	SK-N-SH	brain:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
4	NFIC	chr19:39522314-39523139	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr19:39521624-39523805	K562	blood:	n/a	n/a
6	E2F6	chr19:39522175-39522941	K562	blood:	n/a	n/a
7	MAX	chr19:39521801-39522953	MCF-7	breast:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
8	MAX	chr19:39521563-39523097	A549	lung:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
9	MAX	chr19:39521687-39522911	ECC-1	luminal epithelium:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
10	TCF12	chr19:39522172-39522918	ECC-1	luminal epithelium:	n/a	n/a
11	HMGN3	chr19:39521934-39523312	K562	blood:	n/a	n/a
12	ZBTB7A	chr19:39522212-39523126	ECC-1	luminal epithelium:	n/a	n/a
13	ZBTB7A	chr19:39522125-39523041	ECC-1	luminal epithelium:	n/a	n/a
14	SIN3AK20	chr19:39521478-39523896	PANC-1	pancreas:	n/a	n/a
15	MAX	chr19:39522835-39523565	H1-hESC	embryonic stem cell:	n/a	chr19:39522871-39522881
16	MAX	chr19:39521862-39523558	H1-hESC	embryonic stem cell:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
17	SIN3AK20	chr19:39521601-39523985	PANC-1	pancreas:	n/a	n/a
18	JUND	chr19:39521767-39523036	A549	lung:	n/a	n/a
19	POLR2A	chr19:39520454-39524689	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:39521695-39523527	MCF-7	breast:	n/a	n/a
21	MAX	chr19:39521589-39522954	K562	blood:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
22	TCF12	chr19:39521363-39523919	A549	lung:	n/a	n/a
23	CTCF	chr19:39522518-39522908	K562	blood:	n/a	n/a
24	CREB1	chr19:39522872-39523526	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr19:39522887-39522896	Gliobla	brain:	n/a	n/a
26	ELF1	chr19:39522132-39522891	K562	blood:	n/a	chr19:39522482-39522493 chr19:39522480-39522493
27	FOXA2	chr19:39521716-39522913	A549	lung:	n/a	n/a
28	POLR2A	chr19:39522172-39522982	ProgFib	skin:	n/a	n/a
29	POLR2A	chr19:39522304-39523190	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:39521707-39522923	HCT-116	colon:	n/a	n/a
31	MAX	chr19:39521380-39523937	A549	lung:	n/a	chr19:39522034-39522044 chr19:39522040-39522050 chr19:39522036-39522051 chr19:39522040-39522049 chr19:39522871-39522881 chr19:39522039-39522050 chr19:39522041-39522048
32	POLR2A	chr19:39521711-39523436	A549	lung:	n/a	n/a
33	POLR2A	chr19:39521784-39523389	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:39521674-39522966	HCT-116	colon:	n/a	n/a
35	POLR2A	chr19:39522837-39523509	H1-hESC	embryonic stem cell:	n/a	n/a
36	CCNT2	chr19:39521775-39523522	K562	blood:	n/a	chr19:39523229-39523238 chr19:39522088-39522097 chr19:39522023-39522032
37	E2F6	chr19:39521783-39522967	K562	blood:	n/a	chr19:39522088-39522097
38	REST	chr19:39521568-39523982	PANC-1	pancreas:	n/a	n/a
39	NR2F2	chr19:39522191-39523174	MCF-7	breast:	n/a	n/a
40	POLR2A	chr19:39521660-39523415	MCF-7	breast:	n/a	n/a
41	E2F6	chr19:39521584-39523594	A549	lung:	n/a	chr19:39522088-39522097 chr19:39523144-39523154
42	POLR2A	chr19:39522351-39522935	ECC-1	luminal epithelium:	n/a	n/a
43	HA-E2F1	chr19:39522330-39522926	MCF-7	breast:	n/a	n/a
44	POLR2A	chr19:39521696-39522974	A549	lung:	n/a	n/a
45	MYC	chr19:39522889-39522938	MCF-7	breast:	n/a	n/a
46	UBTF	chr19:39522255-39522945	K562	blood:	n/a	n/a
47	POLR2A	chr19:39519979-39524546	PANC-1	pancreas:	n/a	n/a
48	E2F6	chr19:39522068-39522958	A549	lung:	n/a	chr19:39522088-39522097
49	CREB1	chr19:39521653-39523471	A549	lung:	n/a	n/a
50	SIN3A	chr19:39521612-39523514	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39464957..39467280-chr19:39522120..39523795,2	K562	blood:
2	chr19:39464164..39468178-chr19:39520932..39524285,4	MCF-7	breast:
3	chr19:39521357..39523979-chr19:39614875..39616703,2	MCF-7	breast:

Variant related genes	Relation type
FBXO27	TF binding region
ENSG00000130669	Chromatin interaction
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10406222	0.88[ASN][1000 genomes]
rs10416823	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417436	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424632	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10424827	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426645	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10426661	0.86[ASN][1000 genomes]
rs1062261	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10853723	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10853724	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083499	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083500	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083501	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083502	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1139251	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11667641	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670486	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670520	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11673044	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11673637	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11880441	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883422	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12609806	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610200	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12610248	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12971842	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972850	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12972978	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12978163	0.89[ASN][1000 genomes]
rs12978749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982199	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12982349	0.91[ASN][1000 genomes]
rs12982529	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985447	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1651748	0.84[EUR][1000 genomes]
rs1840745	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840746	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840747	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840748	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864191	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869983	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36154890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280369	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802007	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802009	0.86[ASN][1000 genomes]
rs4803181	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803185	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803186	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803187	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803188	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803193	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58897626	0.87[ASN][1000 genomes]
rs60775146	0.87[ASN][1000 genomes]
rs62119538	0.88[ASN][1000 genomes]
rs628335	0.85[ASN][1000 genomes]
rs6508835	0.88[ASN][1000 genomes]
rs6508836	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508837	0.88[ASN][1000 genomes]
rs6508838	0.91[ASN][1000 genomes]
rs6508839	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508840	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508841	0.91[ASN][1000 genomes]
rs6508842	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508843	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681496	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7247801	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248513	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248652	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250110	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7250431	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251264	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255211	0.93[ASN][1000 genomes]
rs7256126	0.90[ASN][1000 genomes]
rs7258862	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259064	0.86[ASN][1000 genomes]
rs7259197	0.86[ASN][1000 genomes]
rs7259473	0.80[ASN][1000 genomes]
rs7259801	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8100503	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8103187	0.88[ASN][1000 genomes]
rs8104751	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104899	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104990	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105865	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109176	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3848623	FBXO27	cis	Esophagus Mucosa	GTEx
rs3848623	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs3848623	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs3848623	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39521000-39523600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:39521400-39523600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:39521400-39523600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:39521400-39523800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:39521600-39523000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:39521600-39523200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:39521600-39523200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:39521600-39523400	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr19:39521600-39523600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:39521600-39523600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:39521600-39523600	Active TSS	Rectal Smooth Muscle	rectum
12	chr19:39521600-39523800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:39521600-39523800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr19:39521800-39523000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:39521800-39523000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:39521800-39523000	Active TSS	Pancreas	Pancrea
17	chr19:39521800-39523200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:39521800-39523200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
19	chr19:39521800-39523200	Active TSS	Fetal Intestine Large	intestine
20	chr19:39521800-39523200	Transcr. at gene 5' and 3'	Right Atrium	heart
21	chr19:39521800-39523200	Active TSS	HSMM	muscle
22	chr19:39521800-39523400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:39521800-39523400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:39521800-39523400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:39521800-39523400	Active TSS	Brain Substantia Nigra	brain
26	chr19:39521800-39523400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr19:39521800-39523400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:39521800-39523400	Active TSS	HepG2	liver
29	chr19:39521800-39523600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr19:39521800-39523600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39521800-39523600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr19:39521800-39523800	Active TSS	Brain Anterior Caudate	brain
33	chr19:39521800-39523800	Active TSS	Brain Hippocampus Middle	brain
34	chr19:39522000-39523000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:39522000-39523000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:39522000-39523000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:39522000-39523000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr19:39522000-39523000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:39522000-39523000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:39522000-39523000	Active TSS	GM12878-XiMat	blood
41	chr19:39522000-39523200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr19:39522000-39523200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr19:39522000-39523200	Active TSS	Esophagus	oesophagus
44	chr19:39522000-39523200	Active TSS	Fetal Intestine Small	intestine
45	chr19:39522000-39523200	Bivalent/Poised TSS	Fetal Stomach	stomach
46	chr19:39522000-39523200	Bivalent/Poised TSS	Psoas Muscle	Psoas
47	chr19:39522000-39523200	Active TSS	HSMMtube	muscle
48	chr19:39522000-39523200	Active TSS	K562	blood
49	chr19:39522000-39523400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr19:39522000-39523400	Active TSS	HUES6 Cell Line	embryonic stem cell

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