Variant report

Variant	rs7253040
Chromosome Location	chr19:36390341-36390342
allele	C/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	YY1	chr19:36390227-36390887	GM12878	blood:	n/a	chr19:36390660-36390669 chr19:36390654-36390668 chr19:36390788-36390802 chr19:36390658-36390669 chr19:36390789-36390803
2	TAF1	chr19:36390319-36390955	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr19:36390067-36391782	GM12892	blood:	n/a	n/a
4	MYC	chr19:36390265-36390924	MCF10A-Er-Src	breast:	n/a	n/a
5	NFATC1	chr19:36390339-36390946	GM12878	blood:	n/a	n/a
6	MXI1	chr19:36389396-36392037	SK-N-SH	brain:	n/a	n/a
7	TBL1XR1	chr19:36390216-36391772	GM12878	blood:	n/a	n/a
8	ZBTB7A	chr19:36389711-36390345	ECC-1	luminal epithelium:	n/a	n/a
9	TCF12	chr19:36389907-36391960	A549	lung:	n/a	chr19:36390770-36390777 chr19:36391169-36391179
10	USF1	chr19:36390025-36390466	K562	blood:	n/a	chr19:36390267-36390278
11	MAX	chr19:36390093-36390954	GM12878	blood:	n/a	n/a
12	SP1	chr19:36390315-36391095	HCT-116	colon:	n/a	chr19:36390663-36390672 chr19:36390875-36390888 chr19:36390662-36390674 chr19:36390784-36390796 chr19:36390658-36390667 chr19:36390656-36390668 chr19:36390656-36390668 chr19:36390786-36390795 chr19:36390891-36390900 chr19:36390657-36390666 chr19:36390880-36390889
13	POLR2A	chr19:36389078-36391783	GM12878	blood:	n/a	n/a
14	USF1	chr19:36390037-36390459	H1-hESC	embryonic stem cell:	n/a	chr19:36390267-36390278
15	POLR2A	chr19:36389853-36390965	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr19:36390299-36390977	GM12892	blood:	n/a	n/a
17	USF1	chr19:36390059-36390381	H1-hESC	embryonic stem cell:	n/a	chr19:36390267-36390278
18	POLR2A	chr19:36389500-36391774	GM15510	blood:	n/a	n/a
19	POLR2A	chr19:36383824-36391793	GM12878	blood:	n/a	n/a
20	NR2F2	chr19:36389961-36390437	MCF-7	breast:	n/a	n/a
21	NFIC	chr19:36389970-36391040	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:36390068-36391929	K562	blood:	n/a	n/a
23	BCL3	chr19:36390317-36391345	A549	lung:	n/a	chr19:36390656-36390669 chr19:36390658-36390667 chr19:36390834-36390843
24	POLR2A	chr19:36388326-36390442	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:36386218-36391884	GM12878	blood:	n/a	n/a
26	YY1	chr19:36390089-36390943	A549	lung:	n/a	chr19:36390660-36390669 chr19:36390654-36390668 chr19:36390788-36390802 chr19:36390658-36390669 chr19:36390789-36390803
27	ZNF384	chr19:36390024-36390833	GM12878	blood:	n/a	n/a
28	SIN3AK20	chr19:36390290-36391822	PANC-1	pancreas:	n/a	n/a
29	EP300	chr19:36390255-36390955	GM12878	blood:	n/a	chr19:36390838-36390847
30	POLR2A	chr19:36390314-36391838	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:36389440-36391870	GM12892	blood:	n/a	n/a
32	EP300	chr19:36390263-36391797	A549	lung:	n/a	chr19:36391417-36391433 chr19:36391426-36391435 chr19:36390838-36390847
33	POLR2A	chr19:36390325-36392067	HepG2	liver:	n/a	n/a
34	MAX	chr19:36390104-36391896	A549	lung:	n/a	n/a
35	POLR2A	chr19:36389547-36391766	GM19193	blood:	n/a	n/a
36	FOXM1	chr19:36390204-36391680	GM12878	blood:	n/a	n/a
37	GATA3	chr19:36390299-36391757	A549	lung:	n/a	n/a
38	POLR2A	chr19:36390151-36391777	GM12878	blood:	n/a	n/a
39	NR2F2	chr19:36390045-36390806	K562	blood:	n/a	n/a
40	ZNF384	chr19:36390325-36390832	K562	blood:	n/a	n/a
41	YY1	chr19:36390324-36390785	SK-N-SH_RA	brain:	n/a	chr19:36390660-36390669 chr19:36390654-36390668 chr19:36390658-36390669
42	USF1	chr19:36390124-36390433	ECC-1	luminal epithelium:	n/a	chr19:36390267-36390278
43	ELF1	chr19:36389639-36390468	GM12878	blood:	n/a	chr19:36390142-36390153 chr19:36390013-36390026 chr19:36390143-36390152 chr19:36389901-36389910
44	POLR2A	chr19:36389416-36391776	GM18505	blood:	n/a	n/a
45	POLR2A	chr19:36389637-36391900	Hela-S3	cervix:	n/a	n/a
46	RUNX3	chr19:36390226-36390966	GM12878	blood:	n/a	n/a
47	USF2	chr19:36390149-36390377	GM12878	blood:	n/a	n/a
48	ZBTB7A	chr19:36389543-36390360	ECC-1	luminal epithelium:	n/a	n/a
49	YY1	chr19:36390315-36390795	H1-hESC	embryonic stem cell:	n/a	chr19:36390660-36390669 chr19:36390654-36390668 chr19:36390658-36390669
50	FOSL2	chr19:36390341-36391794	A549	lung:	n/a	chr19:36390656-36390665 chr19:36390531-36390540

No.	Distal block	Cell Line	Cell type
1	chr19:36388870..36390539-chr19:36431114..36433630,2	MCF-7	breast:
2	chr19:36134320..36136453-chr19:36390020..36392248,2	MCF-7	breast:
3	chr19:36389776..36392991-chr19:36393581..36401271,10	K562	blood:
4	chr19:36370768..36374759-chr19:36390074..36391659,3	MCF-7	breast:
5	chr19:36334818..36337477-chr19:36389378..36392350,2	MCF-7	breast:
6	chr19:36377925..36382197-chr19:36388677..36391097,3	MCF-7	breast:
7	chr19:36388094..36390635-chr19:36498099..36499853,2	K562	blood:
8	chr19:36379784..36382461-chr19:36387954..36392218,4	MCF-7	breast:
9	chr1:92764062..92764602-chr19:36390162..36391104,2	Hela-S3	cervix:
10	chr19:36247959..36249985-chr19:36390079..36391606,2	MCF-7	breast:
11	chr19:36387498..36389148-chr19:36389747..36391411,2	K562	blood:
12	chr19:36390062..36392033-chr19:36425677..36427196,2	MCF-7	breast:
13	chr19:36390133..36392611-chr19:36392789..36396319,5	MCF-7	breast:
14	chr19:36359272..36362126-chr19:36389056..36392231,3	MCF-7	breast:

Variant related genes	Relation type
HCST	TF binding region
NFKBID	TF binding region
ENSG00000011600	Chromatin interaction
ENSG00000243968	Chromatin interaction
ENSG00000174842	Chromatin interaction
ENSG00000004776	Chromatin interaction
ENSG00000126264	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000122484	Chromatin interaction
ENSG00000126243	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000105290	Chromatin interaction
ENSG00000105672	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11878547	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17173033	0.83[ASN][1000 genomes]
rs17549166	0.83[EUR][1000 genomes]
rs1802029	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230260	0.83[ASN][1000 genomes]
rs33964243	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376240	0.83[ASN][1000 genomes]
rs56264349	0.83[ASN][1000 genomes]
rs58422001	0.91[ASN][1000 genomes]
rs7251744	0.90[ASN][1000 genomes]
rs7251879	0.91[ASN][1000 genomes]
rs7252902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254113	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258214	0.90[ASN][1000 genomes]
rs7258909	0.90[ASN][1000 genomes]
rs8105153	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106480	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106495	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108360	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8108459	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113524	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113704	0.88[ASN][1000 genomes]
rs879407	0.91[ASN][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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 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	chr19:36386800-36391600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:36388600-36392000	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:36388800-36391600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:36389000-36390400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr19:36389000-36391600	Active TSS	Gastric	stomach
6	chr19:36389000-36391800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:36389000-36391800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:36389000-36391800	Active TSS	NHDF-Ad	bronchial
9	chr19:36389000-36392000	Active TSS	Brain Angular Gyrus	brain
10	chr19:36389000-36392000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:36389000-36392000	Active TSS	NHLF	lung
12	chr19:36389200-36390400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:36389200-36390400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr19:36389200-36390400	Enhancers	Fetal Brain Male	brain
15	chr19:36389200-36391400	Active TSS	Fetal Brain Female	brain
16	chr19:36389200-36391800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:36389200-36391800	Active TSS	Osteobl	bone
18	chr19:36389200-36392000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:36389200-36392000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr19:36389200-36392000	Flanking Active TSS	Placenta	Placenta
21	chr19:36389200-36392200	Active TSS	Right Atrium	heart
22	chr19:36389400-36390400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:36389400-36390400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr19:36389400-36390400	Flanking Active TSS	HUVEC	blood vessel
25	chr19:36389400-36390600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr19:36389400-36390600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36389400-36391600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr19:36389400-36391600	Active TSS	Esophagus	oesophagus
29	chr19:36389400-36391600	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr19:36389400-36391800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:36389400-36391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:36389400-36391800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:36389400-36391800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:36389400-36391800	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr19:36389400-36391800	Active TSS	Aorta	Aorta
36	chr19:36389400-36391800	Active TSS	Ovary	ovary
37	chr19:36389400-36391800	Active TSS	Psoas Muscle	Psoas
38	chr19:36389400-36391800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr19:36389400-36392000	Active TSS	H9 Cell Line	embryonic stem cell
40	chr19:36389400-36392000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:36389400-36392000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr19:36389400-36392000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:36389400-36392000	Active TSS	Primary T cells from cord blood	blood
44	chr19:36389400-36392000	Active TSS	HSMMtube	muscle
45	chr19:36389600-36390400	Flanking Active TSS	Dnd41	blood
46	chr19:36389600-36391400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr19:36389600-36391400	Active TSS	HMEC	breast
48	chr19:36389600-36391600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr19:36389600-36391600	Active TSS	Small Intestine	intestine
50	chr19:36389600-36391800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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