Variant report

Variant	rs3786949
Chromosome Location	chr19:39826479-39826480
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	POLR2A	chr19:39825971-39826927	GM19099	blood:	n/a	n/a
2	STAT5A	chr19:39826446-39826963	GM12878	blood:	n/a	chr19:39826782-39826794 chr19:39826502-39826514
3	GABPA	chr19:39826311-39826958	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:39825908-39826905	GM18505	blood:	n/a	n/a
5	POLR2A	chr19:39825969-39826880	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39826423-39826483	K562	blood:	n/a	n/a
7	MAZ	chr19:39825886-39826915	GM12878	blood:	n/a	n/a
8	MYC	chr19:39825954-39826900	NB4	blood:	n/a	n/a
9	POLR2A	chr19:39825926-39826980	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:39826379-39826824	K562	blood:	n/a	n/a
11	POLR2A	chr19:39825776-39826855	K562	blood:	n/a	n/a
12	POLR2A	chr19:39825749-39826921	GM12878	blood:	n/a	n/a
13	GABPA	chr19:39826260-39827053	K562	blood:	n/a	n/a
14	GABPA	chr19:39826372-39826934	HL-60	blood:	n/a	n/a
15	POLR2A	chr19:39825834-39826902	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39825651-39826923	GM12892	blood:	n/a	n/a
17	EP300	chr19:39826300-39826912	GM12878	blood:	n/a	n/a
18	MTA3	chr19:39825664-39827000	GM12878	blood:	n/a	n/a
19	MAX	chr19:39825932-39826921	NB4	blood:	n/a	n/a
20	ELF1	chr19:39826009-39827004	GM12878	blood:	n/a	chr19:39826429-39826442
21	TAF1	chr19:39826248-39826869	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39825812-39827105	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:39825895-39826924	GM12878	blood:	n/a	n/a
24	PML	chr19:39825805-39826985	GM12878	blood:	n/a	n/a
25	RUNX3	chr19:39825836-39826979	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:39825868-39826923	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:39825912-39826952	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:39826085-39826827	GM19193	blood:	n/a	n/a
29	TBP	chr19:39826306-39826902	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:39825938-39826849	NB4	blood:	n/a	n/a
31	SP1	chr19:39826239-39826540	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:39826268-39826833	GM12891	blood:	n/a	n/a
33	MAX	chr19:39826024-39826922	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:39826471-39826904	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr19:39826293-39826909	Raji	blood:	n/a	n/a
36	POLR2A	chr19:39825903-39826921	GM12892	blood:	n/a	n/a
37	POLR2A	chr19:39826004-39826810	GM15510	blood:	n/a	n/a
38	POLR2A	chr19:39825864-39826994	HL-60	blood:	n/a	n/a
39	RUNX3	chr19:39825844-39826991	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:39825953-39826484	GM12892	blood:	n/a	n/a
41	POLR2A	chr19:39825763-39826897	GM12892	blood:	n/a	n/a
42	POLR2A	chr19:39825797-39826898	GM12878	blood:	n/a	n/a
43	PML	chr19:39826438-39826874	K562	blood:	n/a	n/a
44	POLR2A	chr19:39826279-39826862	K562	blood:	n/a	n/a
45	POU2F2	chr19:39826231-39826556	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:39825936-39826988	GM18951	blood:	n/a	n/a
47	POLR2A	chr19:39825676-39827072	GM12878	blood:	n/a	n/a
48	SPI1	chr19:39826157-39826919	HL-60	blood:	n/a	chr19:39826688-39826701 chr19:39826772-39826785
49	ELF1	chr19:39825969-39826983	K562	blood:	n/a	chr19:39826429-39826442

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39826340..39829691-chr19:39831267..39834495,5	K562	blood:
2	chr19:39826203..39828584-chr19:39871220..39872824,2	K562	blood:

Variant related genes	Relation type
GMFG	TF binding region
ENSG00000269246	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1375910	1.00[JPT][hapmap]
rs16973342	1.00[JPT][hapmap]
rs16973348	1.00[JPT][hapmap]
rs16973350	1.00[JPT][hapmap]
rs16973363	1.00[JPT][hapmap]
rs16973374	1.00[JPT][hapmap]
rs2067102	1.00[JPT][hapmap]
rs2074852	1.00[JPT][hapmap]
rs251906	0.83[JPT][hapmap]
rs30453	0.91[JPT][hapmap]
rs30454	0.91[JPT][hapmap]
rs30455	0.91[JPT][hapmap]
rs30457	0.91[JPT][hapmap]
rs36264	0.91[JPT][hapmap]
rs36270	0.83[JPT][hapmap]
rs3826938	1.00[JPT][hapmap]
rs3865515	1.00[JPT][hapmap]
rs40353	0.83[JPT][hapmap]
rs40441	0.91[JPT][hapmap]
rs562638	0.91[JPT][hapmap]
rs6508860	0.91[JPT][hapmap]
rs685125	0.83[JPT][hapmap]
rs917319	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833830	chr19:39709538-39837846	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
4	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
6	nsv911681	chr19:39797716-39856246	Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39818600-39831600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr19:39818800-39826800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:39823800-39831200	Weak transcription	A549	lung
4	chr19:39825000-39827000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:39825200-39826800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:39825200-39827000	Active TSS	Duodenum Mucosa	Duodenum
7	chr19:39825200-39827000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr19:39825400-39826600	Active TSS	Colonic Mucosa	Colon
9	chr19:39825400-39826800	Active TSS	GM12878-XiMat	blood
10	chr19:39825400-39827000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:39825400-39827000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr19:39825600-39826600	Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr19:39825600-39826600	Active TSS	Esophagus	oesophagus
14	chr19:39825600-39826600	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:39825600-39826800	Active TSS	Primary T cells from cord blood	blood
16	chr19:39825600-39826800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr19:39825600-39826800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:39825600-39826800	Active TSS	Brain Hippocampus Middle	brain
19	chr19:39825600-39826800	Active TSS	Fetal Thymus	thymus
20	chr19:39825600-39826800	Active TSS	Right Ventricle	heart
21	chr19:39825600-39826800	Active TSS	Thymus	Thymus
22	chr19:39825600-39827000	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr19:39825800-39826600	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr19:39825800-39826600	Active TSS	Liver	Liver
25	chr19:39825800-39826600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:39825800-39826600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr19:39825800-39826600	Active TSS	Fetal Muscle Trunk	muscle
28	chr19:39825800-39826600	Active TSS	Fetal Muscle Leg	muscle
29	chr19:39825800-39826600	Active TSS	Placenta	Placenta
30	chr19:39825800-39826600	Active TSS	Lung	lung
31	chr19:39825800-39826600	Active TSS	Pancreas	Pancrea
32	chr19:39825800-39826600	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr19:39825800-39826600	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr19:39825800-39826600	Active TSS	Small Intestine	intestine
35	chr19:39825800-39826600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
36	chr19:39825800-39826800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:39825800-39826800	Active TSS	Primary monocytes fromperipheralblood	blood
38	chr19:39825800-39826800	Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr19:39825800-39826800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:39825800-39826800	Bivalent/Poised TSS	Fetal Stomach	stomach
41	chr19:39825800-39826800	Active TSS	Left Ventricle	heart
42	chr19:39825800-39826800	Active TSS	Right Atrium	heart
43	chr19:39825800-39826800	Active TSS	Dnd41	blood
44	chr19:39825800-39826800	Active TSS	NHLF	lung
45	chr19:39825800-39827000	Active TSS	Adipose Nuclei	Adipose
46	chr19:39825800-39827000	Active TSS	Spleen	Spleen
47	chr19:39826000-39826600	Active TSS	Primary B cells from peripheral blood	blood
48	chr19:39826000-39826600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:39826000-39826600	Active TSS	Fetal Intestine Large	intestine
50	chr19:39826000-39826600	Active TSS	Fetal Intestine Small	intestine

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