Variant report

Variant	rs12974617
Chromosome Location	chr19:56090493-56090494
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56090422-56090536	A549	lung:	n/a	n/a
2	POLR2A	chr19:56090329-56090623	A549	lung:	n/a	n/a
3	POLR2A	chr19:56089868-56091088	A549	lung:	n/a	n/a
4	EGR1	chr19:56090301-56091039	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:56090394-56090741	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56085801..56089181-chr19:56090146..56094195,5	MCF-7	breast:
2	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
3	chr19:56076616..56078313-chr19:56088787..56090501,2	K562	blood:
4	chr19:56089123..56090949-chr2:85134145..85135899,2	MCF-7	breast:
5	chr19:56089635..56093860-chr19:56114549..56117863,7	MCF-7	breast:
6	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267730	TF binding region
ENSG00000267730	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403462	0.82[ASN][1000 genomes]
rs10451452	0.83[ASN][1000 genomes]
rs1079082	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079083	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079084	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1079085	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084402	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11665826	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668725	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11668729	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11669682	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879347	0.95[ASN][1000 genomes]
rs12610510	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610512	0.99[ASN][1000 genomes]
rs12610709	0.92[ASN][1000 genomes]
rs12610881	0.95[ASN][1000 genomes]
rs12972159	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12978375	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12979354	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12979366	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980543	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014329	0.92[ASN][1000 genomes]
rs2864433	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2902748	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34174244	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34715654	0.85[ASN][1000 genomes]
rs34937940	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35088354	0.85[ASN][1000 genomes]
rs35197282	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35522245	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35839536	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36047579	0.93[ASN][1000 genomes]
rs60220392	0.93[ASN][1000 genomes]
rs71368855	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs71368856	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7246944	0.93[ASN][1000 genomes]
rs7251733	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	esv3388302	chr19:56088140-56092838	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv3423073	chr19:56088190-56091888	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3437537	chr19:56088665-56091513	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56076000-56091000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56076000-56091000	Weak transcription	Right Atrium	heart
3	chr19:56076600-56091000	Weak transcription	Fetal Heart	heart
4	chr19:56078600-56091000	Weak transcription	Fetal Kidney	kidney
5	chr19:56081800-56091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:56083800-56091000	Weak transcription	HepG2	liver
7	chr19:56084200-56091000	Weak transcription	K562	blood
8	chr19:56086000-56091000	Weak transcription	NH-A	brain
9	chr19:56086200-56091000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:56086200-56091200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:56086400-56091200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:56086600-56091000	Weak transcription	Fetal Brain Male	brain
13	chr19:56086600-56091400	Weak transcription	Primary T cells from cord blood	blood
14	chr19:56086800-56090600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:56086800-56091000	Weak transcription	Brain Substantia Nigra	brain
16	chr19:56086800-56091000	Weak transcription	HMEC	breast
17	chr19:56087000-56091000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr19:56087000-56091200	Weak transcription	Stomach Mucosa	stomach
19	chr19:56087200-56091000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr19:56087200-56091000	Weak transcription	GM12878-XiMat	blood
21	chr19:56087200-56091200	Weak transcription	Fetal Thymus	thymus
22	chr19:56087400-56090600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:56087400-56090600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:56087400-56090600	Strong transcription	Fetal Brain Female	brain
25	chr19:56087600-56090600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:56087600-56090600	Strong transcription	Fetal Stomach	stomach
27	chr19:56087600-56090800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:56087600-56090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:56087600-56091400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:56087800-56090800	Weak transcription	Hela-S3	cervix
31	chr19:56088000-56090600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:56088000-56090600	Strong transcription	Dnd41	blood
33	chr19:56088200-56090600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:56088200-56090600	Strong transcription	Adipose Nuclei	Adipose
35	chr19:56088200-56090800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr19:56088200-56090800	Strong transcription	NHLF	lung
37	chr19:56088200-56091000	Weak transcription	Brain Angular Gyrus	brain
38	chr19:56088400-56090800	Strong transcription	Thymus	Thymus
39	chr19:56088400-56091200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:56088600-56090600	Strong transcription	Colonic Mucosa	Colon
41	chr19:56088800-56090800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:56088800-56091000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:56088800-56091200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:56089000-56090800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:56089000-56091000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:56089000-56091000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:56089000-56091000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:56089000-56091200	Weak transcription	Liver	Liver
49	chr19:56089200-56090600	ZNF genes & repeats	Spleen	Spleen
50	chr19:56089200-56090800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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