Variant report

Variant	rs17217098
Chromosome Location	chr19:19702384-19702385
allele	A/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	chr19:19701916-19702401	GM12878	blood:	n/a	n/a
2	CUX1	chr19:19701955-19702426	GM12878	blood:	n/a	n/a
3	RELA	chr19:19701867-19702401	GM10847	blood:	n/a	chr19:19702076-19702085 chr19:19702076-19702085
4	MYC	chr19:19701804-19702392	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr19:19701921-19702439	MCF-7	breast:	n/a	n/a
6	TBL1XR1	chr19:19701807-19702695	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:19701600-19702987	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:19702019-19702592	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:19702356-19702384	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:19701833-19702669	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:19702256-19702613	GM12878	blood:	n/a	n/a
12	MTA3	chr19:19701787-19702736	GM12878	blood:	n/a	n/a
13	SMC3	chr19:19701877-19702515	Hela-S3	cervix:	n/a	n/a
14	PBX3	chr19:19702380-19702640	GM12878	blood:	n/a	chr19:19702526-19702535
15	EBF1	chr19:19701855-19702626	GM12878	blood:	n/a	chr19:19702359-19702368 chr19:19702357-19702368 chr19:19702358-19702368
16	EBF1	chr19:19701744-19702696	GM12878	blood:	n/a	chr19:19702359-19702368 chr19:19702357-19702368 chr19:19702358-19702368
17	STAT3	chr19:19701818-19702397	GM12878	blood:	n/a	chr19:19702108-19702116 chr19:19702039-19702048
18	GATA3	chr19:19701734-19702458	MCF-7	breast:	n/a	chr19:19702041-19702050 chr19:19701899-19701909
19	STAT5A	chr19:19701909-19702423	GM12878	blood:	n/a	chr19:19702108-19702116 chr19:19702039-19702048
20	FOXM1	chr19:19701784-19702525	GM12878	blood:	n/a	n/a
21	SMC3	chr19:19701961-19702451	GM12878	blood:	n/a	n/a
22	CEBPB	chr19:19701956-19702428	A549	lung:	n/a	n/a
23	CHD2	chr19:19701936-19702466	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:19702055-19702593	GM12878	blood:	n/a	n/a
25	RELA	chr19:19701783-19702547	GM19099	blood:	n/a	chr19:19702076-19702085 chr19:19702076-19702085
26	POLR2A	chr19:19702040-19702416	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr19:19701651-19702769	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:19701639-19702684	GM12878	blood:	n/a	n/a
29	PML	chr19:19701750-19702512	GM12878	blood:	n/a	n/a
30	MTA3	chr19:19701798-19702700	GM12878	blood:	n/a	n/a
31	CEBPB	chr19:19701789-19702580	GM12878	blood:	n/a	n/a
32	FOXP2	chr19:19702115-19702462	SK-N-MC	brain:	n/a	n/a
33	MAX	chr19:19701884-19702691	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr19:19701844-19702559	GM18505	blood:	n/a	n/a
35	NR3C1	chr19:19702101-19702412	A549	lung:	n/a	n/a
36	FOSL2	chr19:19701755-19702397	SK-N-SH	brain:	n/a	chr19:19702039-19702049 chr19:19702039-19702048 chr19:19702039-19702049 chr19:19702039-19702049 chr19:19702041-19702052
37	FOXA1	chr19:19702073-19702390	T-47D	breast:	n/a	n/a
38	ELF1	chr19:19701896-19702385	GM12878	blood:	n/a	n/a
39	JUND	chr19:19701606-19702559	SK-N-SH	brain:	n/a	chr19:19702531-19702538 chr19:19702039-19702049 chr19:19702039-19702048 chr19:19702038-19702049 chr19:19702039-19702049 chr19:19702039-19702049 chr19:19702041-19702052
40	RUNX3	chr19:19701830-19702691	GM12878	blood:	n/a	n/a
41	CEBPB	chr19:19701652-19702611	Hela-S3	cervix:	n/a	n/a
42	STAT3	chr19:19702003-19702416	MCF10A-Er-Src	breast:	n/a	chr19:19702108-19702116 chr19:19702039-19702048
43	POLR2A	chr19:19701595-19702812	GM12892	blood:	n/a	n/a
44	NR3C1	chr19:19701902-19702547	A549	lung:	n/a	n/a
45	SMARCC1	chr19:19701726-19702519	Hela-S3	cervix:	n/a	chr19:19702039-19702048
46	CHD1	chr19:19701901-19702539	GM12878	blood:	n/a	n/a
47	MAX	chr19:19702052-19702736	GM12878	blood:	n/a	n/a
48	TFAP2C	chr19:19701640-19702438	Hela-S3	cervix:	n/a	chr19:19702046-19702061
49	MAZ	chr19:19701905-19702513	GM12878	blood:	n/a	n/a
50	EBF1	chr19:19701811-19702629	GM12878	blood:	n/a	chr19:19702359-19702368 chr19:19702357-19702368 chr19:19702358-19702368

No.	Distal block	Cell Line	Cell type
1	chr19:19702026..19704512-chr19:19777801..19779336,2	MCF-7	breast:
2	chr19:19699647..19703848-chr19:19728208..19731865,4	MCF-7	breast:
3	chr19:19701585..19704571-chr19:19749702..19751858,2	K562	blood:
4	chr19:19700624..19702587-chr19:19705452..19707616,2	MCF-7	breast:
5	chr19:19699149..19708161-chr19:19735507..19742255,11	MCF-7	breast:
6	chr19:19660487..19662090-chr19:19700692..19703512,2	MCF-7	breast:
7	chr19:19701600..19702494-chr19:19738189..19739163,2	MCF-7	breast:
8	chr19:19701845..19703912-chr19:19706648..19708750,2	K562	blood:

Variant related genes	Relation type
PHF5CP	TF binding region
ENSG00000105717	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10500212	0.87[EUR][1000 genomes]
rs12608729	0.87[EUR][1000 genomes]
rs12610185	0.87[EUR][1000 genomes]
rs12610191	0.87[EUR][1000 genomes]
rs16996185	0.87[EUR][1000 genomes]
rs57504626	0.87[EUR][1000 genomes]
rs58847337	0.87[EUR][1000 genomes]
rs73004926	0.83[EUR][1000 genomes]
rs73004933	0.83[EUR][1000 genomes]
rs73004951	0.82[EUR][1000 genomes]
rs73004959	0.87[EUR][1000 genomes]
rs73004962	0.87[EUR][1000 genomes]
rs73004966	0.86[EUR][1000 genomes]
rs73004967	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73004975	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
2	chr19:19681600-19703200	Weak transcription	Dnd41	blood
3	chr19:19698800-19708400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:19699000-19703200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr19:19699400-19702400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:19699400-19702800	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr19:19699400-19703000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:19700200-19702600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:19700400-19702600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr19:19700400-19703000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:19700600-19702400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:19700600-19702600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:19700600-19702800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:19700600-19708600	Strong transcription	Thymus	Thymus
15	chr19:19700800-19704000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:19701000-19702600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:19701000-19702600	Enhancers	Duodenum Mucosa	Duodenum
18	chr19:19701000-19703200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr19:19701000-19703200	Enhancers	HMEC	breast
20	chr19:19701200-19702600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:19701200-19703200	Weak transcription	Ovary	ovary
22	chr19:19701400-19702600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr19:19701400-19702600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr19:19701400-19702600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr19:19701400-19702800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr19:19701400-19702800	Enhancers	Stomach Mucosa	stomach
27	chr19:19701400-19703400	Enhancers	Fetal Muscle Leg	muscle
28	chr19:19701400-19703800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:19701600-19702400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:19701600-19702600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:19701600-19702600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr19:19701600-19702600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:19701600-19702600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr19:19701600-19702600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:19701600-19702600	Enhancers	Colon Smooth Muscle	Colon
36	chr19:19701600-19702600	Enhancers	Esophagus	oesophagus
37	chr19:19701600-19702600	Enhancers	Fetal Thymus	thymus
38	chr19:19701600-19702600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr19:19701600-19702600	Enhancers	A549	lung
40	chr19:19701600-19702600	Enhancers	HSMM	muscle
41	chr19:19701600-19702600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr19:19701600-19702600	Enhancers	NH-A	brain
43	chr19:19701600-19702800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:19701600-19702800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:19701600-19702800	Enhancers	Fetal Intestine Large	intestine
46	chr19:19701600-19702800	Flanking Active TSS	Hela-S3	cervix
47	chr19:19701600-19703000	Enhancers	Primary B cells from peripheral blood	blood
48	chr19:19701600-19703000	Enhancers	Fetal Brain Male	brain
49	chr19:19701600-19703200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:19701600-19703200	Enhancers	Fetal Stomach	stomach

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