Variant report

Variant	rs251906
Chromosome Location	chr19:39826838-39826839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:101)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:101 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr19:39826656-39826908	GM12878	blood:	n/a	n/a
2	EGR1	chr19:39826580-39826861	GM12878	blood:	n/a	chr19:39826700-39826714 chr19:39826687-39826697
3	ELF1	chr19:39826575-39827014	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39825971-39826927	GM19099	blood:	n/a	n/a
5	STAT5A	chr19:39826446-39826963	GM12878	blood:	n/a	chr19:39826782-39826794 chr19:39826502-39826514
6	GABPA	chr19:39826311-39826958	HL-60	blood:	n/a	n/a
7	GABPA	chr19:39826483-39826959	K562	blood:	n/a	n/a
8	POLR2A	chr19:39825908-39826905	GM18505	blood:	n/a	n/a
9	POLR2A	chr19:39825969-39826880	GM12878	blood:	n/a	n/a
10	MAZ	chr19:39825886-39826915	GM12878	blood:	n/a	n/a
11	SRF	chr19:39826635-39826876	GM12878	blood:	n/a	chr19:39826687-39826697
12	MYC	chr19:39825954-39826900	NB4	blood:	n/a	n/a
13	TBL1XR1	chr19:39826669-39826934	K562	blood:	n/a	n/a
14	POLR2A	chr19:39825926-39826980	GM12891	blood:	n/a	n/a
15	STAT3	chr19:39826711-39826865	GM12878	blood:	n/a	chr19:39826782-39826794
16	POLR2A	chr19:39825776-39826855	K562	blood:	n/a	n/a
17	SPI1	chr19:39826527-39826891	GM12891	blood:	n/a	chr19:39826688-39826701 chr19:39826772-39826785
18	RCOR1	chr19:39826612-39827026	K562	blood:	n/a	n/a
19	CHD2	chr19:39826632-39826898	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:39825749-39826921	GM12878	blood:	n/a	n/a
21	ETS1	chr19:39826524-39826892	GM12878	blood:	n/a	chr19:39826726-39826737 chr19:39826772-39826783
22	GABPA	chr19:39826598-39826844	GM12878	blood:	n/a	n/a
23	RCOR1	chr19:39826718-39826898	K562	blood:	n/a	n/a
24	NFIC	chr19:39826545-39826868	GM12878	blood:	n/a	n/a
25	MAZ	chr19:39826574-39826906	K562	blood:	n/a	n/a
26	SRF	chr19:39826494-39826873	GM12878	blood:	n/a	chr19:39826687-39826697
27	GABPA	chr19:39826260-39827053	K562	blood:	n/a	n/a
28	SRF	chr19:39826643-39826862	GM12878	blood:	n/a	chr19:39826687-39826697
29	GABPA	chr19:39826372-39826934	HL-60	blood:	n/a	n/a
30	TCF12	chr19:39826584-39826865	GM12878	blood:	n/a	n/a
31	ETS1	chr19:39826571-39826882	K562	blood:	n/a	chr19:39826726-39826737 chr19:39826772-39826783
32	POLR2A	chr19:39825834-39826902	GM12878	blood:	n/a	n/a
33	SPI1	chr19:39826642-39826883	K562	blood:	n/a	chr19:39826688-39826701 chr19:39826772-39826785
34	POLR2A	chr19:39825651-39826923	GM12892	blood:	n/a	n/a
35	SIN3AK20	chr19:39826607-39826881	K562	blood:	n/a	n/a
36	EP300	chr19:39826300-39826912	GM12878	blood:	n/a	n/a
37	MTA3	chr19:39825664-39827000	GM12878	blood:	n/a	n/a
38	MAX	chr19:39825932-39826921	NB4	blood:	n/a	n/a
39	ELF1	chr19:39826009-39827004	GM12878	blood:	n/a	chr19:39826429-39826442
40	TAF1	chr19:39826248-39826869	GM12878	blood:	n/a	n/a
41	ZNF143	chr19:39826666-39827006	K562	blood:	n/a	chr19:39826687-39826705 chr19:39826773-39826792
42	HCFC1	chr19:39826707-39826907	K562	blood:	n/a	n/a
43	BCL11A	chr19:39826558-39826903	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:39825812-39827105	HL-60	blood:	n/a	n/a
45	EP300	chr19:39826617-39826913	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:39825895-39826924	GM12878	blood:	n/a	n/a
47	YY1	chr19:39826576-39826839	K562	blood:	n/a	n/a
48	POLR2A	chr19:39826515-39826931	HUVEC	blood vessel:	n/a	n/a
49	PML	chr19:39825805-39826985	GM12878	blood:	n/a	n/a
50	TEAD4	chr19:39826536-39826968	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39826821-39826871	IMR90	lung:	fetal
2	chr19:39826821-39826871	MCF10A-Er-Src	breast:	n/a
3	chr19:39826821-39826871	MCF-7	breast:	n/a
4	chr19:39826821-39826871	AG04449	skin:	fetal
5	chr19:39826821-39826871	AG10803	skin:	n/a
6	chr19:39826821-39826871	NH-A	brain:	n/a
7	chr19:39826821-39826871	H1-hESC	embryonic stem cell:	embryo
8	chr19:39826821-39826871	Caco-2	colon:	n/a
9	chr19:39826821-39826871	NHBE	bronchial:	n/a
10	chr19:39826821-39826871	PANC-1	pancreas:	n/a
11	chr19:39826821-39826871	NHDF-neo	bronchial:	n/a
12	chr19:39826821-39826871	LNCaP	prostate:	n/a
13	chr19:39826821-39826871	HEEpiC	esophagus:	n/a
14	chr19:39826821-39826871	BJ	skin:	n/a
15	chr19:39826821-39826871	AoSMC	blood vessel:	n/a
16	chr19:39826821-39826871	NT2-D1	testis:	n/a
17	chr19:39826821-39826871	U87	brain:	n/a
18	chr19:39826821-39826871	NB4	blood:	n/a
19	chr19:39826821-39826871	SAEC	small airway:	n/a
20	chr19:39826821-39826871	AG09309	skin:	n/a
21	chr19:39826821-39826871	HPAEpiC	pulmonary alveolar:	n/a
22	chr19:39826821-39826871	GM12878	blood:	n/a
23	chr19:39826821-39826871	HNPCEpiC	eye:	n/a
24	chr19:39826821-39826871	HRE	kidney:	n/a
25	chr19:39826821-39826871	AG09319	gingival:	n/a
26	chr19:39826821-39826871	Hela-S3	cervix:	n/a
27	chr19:39826821-39826871	ECC-1	luminal epithelium:	n/a
28	chr19:39826821-39826871	HRPEpiC	eye:	n/a
29	chr19:39826821-39826871	PrEC	prostate:	n/a
30	chr19:39826821-39826871	CMK	blood:	n/a
31	chr19:39826821-39826871	HCF	heart:	n/a
32	chr19:39826821-39826871	Hepatocyte	liver:	n/a
33	chr19:39826821-39826871	SK-N-SH_RA	brain:	n/a
34	chr19:39826821-39826871	HCPEpiC	choroid plexus:	n/a
35	chr19:39826821-39826871	Jurkat	blood:	n/a
36	chr19:39826821-39826871	SK-N-MC	brain:	n/a
37	chr19:39826821-39826871	HCT-116	colon:	n/a
38	chr19:39826821-39826871	T-47D	breast:	n/a
39	chr19:39826821-39826871	GM12891	blood:	n/a
40	chr19:39826821-39826871	RPTEC	kidney:	n/a
41	chr19:39826821-39826871	SK-N-SH	brain:	n/a
42	chr19:39826821-39826871	HCM	heart:	n/a
43	chr19:39826821-39826871	HUVEC	blood vessel:	n/a
44	chr19:39826821-39826871	HEK293	kidney:	embryo
45	chr19:39826821-39826871	BE2_C	brain:	n/a
46	chr19:39826821-39826871	HAEpiC	amniotic membrane:	n/a
47	chr19:39826821-39826871	GM06990	blood:	n/a
48	chr19:39826821-39826871	HepG2	liver:	n/a
49	chr19:39826821-39826871	HMEC	breast:	n/a
50	chr19:39826821-39826871	HIPEpiC	eye:	n/a

(count:2 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1375910	0.83[JPT][hapmap]
rs16973342	0.83[JPT][hapmap]
rs16973348	0.83[JPT][hapmap]
rs16973350	0.83[JPT][hapmap]
rs16973363	0.83[JPT][hapmap]
rs16973374	0.81[JPT][hapmap]
rs194016	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2067102	0.83[JPT][hapmap]
rs2074852	0.83[JPT][hapmap]
rs251907	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668750	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs30453	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs30454	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs30455	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs30457	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs34605107	0.82[ASN][1000 genomes]
rs34615060	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs36264	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs36270	0.83[JPT][hapmap]
rs3786949	0.83[JPT][hapmap]
rs3826938	0.81[JPT][hapmap]
rs3865515	0.83[JPT][hapmap]
rs40353	0.83[JPT][hapmap]
rs40441	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs562638	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6508860	0.92[JPT][hapmap]
rs685125	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs917319	0.92[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:66 , 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	chr19:39823800-39831200	Weak transcription	A549	lung
3	chr19:39825000-39827000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr19:39825200-39827000	Active TSS	Duodenum Mucosa	Duodenum
5	chr19:39825200-39827000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr19:39825400-39827000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:39825400-39827000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:39825600-39827000	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr19:39825800-39827000	Active TSS	Adipose Nuclei	Adipose
10	chr19:39825800-39827000	Active TSS	Spleen	Spleen
11	chr19:39826200-39827000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:39826400-39828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:39826400-39831400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39826400-39831400	Weak transcription	Brain Angular Gyrus	brain
15	chr19:39826400-39831400	Weak transcription	Brain Anterior Caudate	brain
16	chr19:39826400-39831400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr19:39826400-39831400	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:39826600-39827000	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr19:39826600-39827000	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr19:39826600-39827000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr19:39826600-39827000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:39826600-39827000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr19:39826600-39827200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:39826600-39827200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr19:39826600-39827400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:39826600-39828600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr19:39826600-39830400	Weak transcription	Fetal Intestine Small	intestine
28	chr19:39826600-39830600	Weak transcription	Liver	Liver
29	chr19:39826600-39830600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:39826600-39830600	Weak transcription	Fetal Intestine Large	intestine
31	chr19:39826600-39830800	Weak transcription	Lung	lung
32	chr19:39826600-39831400	Weak transcription	Small Intestine	intestine
33	chr19:39826600-39831600	Weak transcription	Esophagus	oesophagus
34	chr19:39826800-39827000	Enhancers	H9 Cell Line	embryonic stem cell
35	chr19:39826800-39827000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr19:39826800-39827000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr19:39826800-39827000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr19:39826800-39827000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:39826800-39827000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:39826800-39827000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:39826800-39827000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:39826800-39827000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr19:39826800-39827000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39826800-39827000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39826800-39827000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:39826800-39827000	Enhancers	Placenta	Placenta
47	chr19:39826800-39827000	Flanking Active TSS	Fetal Thymus	thymus
48	chr19:39826800-39827000	Flanking Active TSS	Thymus	Thymus
49	chr19:39826800-39827000	Flanking Active TSS	Dnd41	blood
50	chr19:39826800-39827000	Flanking Active TSS	GM12878-XiMat	blood

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