Variant report

Variant	rs57544196
Chromosome Location	chr19:56192201-56192202
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	POLR2A	chr19:56191994-56192308	K562	blood:	n/a	n/a
2	POLR2A	chr19:56191630-56193111	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:56191791-56192206	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56192158-56192613	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:56191201-56192589	K562	blood:	n/a	n/a
6	POLR2A	chr19:56191986-56192361	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56189741..56193540-chr19:56204383..56209311,7	K562	blood:

Variant related genes	Relation type
ENSG00000211571	TF binding region
ENSG00000267117	Chromatin interaction
ENSG00000203305	Chromatin interaction
ENSG00000267018	Chromatin interaction
ENSG00000267183	Chromatin interaction
ENSG00000063244	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10402618	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10403866	0.98[ASN][1000 genomes]
rs10408613	0.88[ASN][1000 genomes]
rs10410404	0.84[ASN][1000 genomes]
rs10410802	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10410886	0.89[ASN][1000 genomes]
rs10412050	0.86[ASN][1000 genomes]
rs10415521	0.96[ASN][1000 genomes]
rs10417539	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421319	0.83[ASN][1000 genomes]
rs11882031	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2280255	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28375493	0.83[EUR][1000 genomes]
rs28385383	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28595590	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28668166	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310437	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs310441	0.89[ASN][1000 genomes]
rs3745446	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs523509	0.82[ASN][1000 genomes]
rs575274	0.83[EUR][1000 genomes]
rs584405	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58490076	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60873246	0.89[ASN][1000 genomes]
rs610811	0.83[EUR][1000 genomes]
rs617073	0.89[ASN][1000 genomes]
rs648651	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs681804	0.89[ASN][1000 genomes]
rs7256441	0.84[ASN][1000 genomes]
rs73613281	0.98[ASN][1000 genomes]
rs8100143	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8104242	0.95[ASN][1000 genomes]
rs8109983	0.95[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	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
2	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
3	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
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56187800-56192400	Genic enhancers	Placenta	Placenta
2	chr19:56188000-56192400	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr19:56188200-56192800	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:56188400-56193200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:56188400-56193800	Strong transcription	Brain Cingulate Gyrus	brain
7	chr19:56188400-56194000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:56188600-56192800	Genic enhancers	Gastric	stomach
12	chr19:56188600-56193000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:56188600-56194000	Strong transcription	A549	lung
14	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
17	chr19:56188800-56192800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:56188800-56194000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
20	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
21	chr19:56189000-56192600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
22	chr19:56189000-56193400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:56189000-56193400	Genic enhancers	Spleen	Spleen
24	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
25	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
26	chr19:56189200-56193200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr19:56189200-56193400	Genic enhancers	Stomach Mucosa	stomach
28	chr19:56189200-56195200	Genic enhancers	Fetal Intestine Small	intestine
29	chr19:56189200-56195400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:56189200-56199400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:56189400-56192400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:56189400-56192400	Genic enhancers	Right Ventricle	heart
35	chr19:56189400-56192600	Strong transcription	Aorta	Aorta
36	chr19:56189400-56192600	Genic enhancers	Pancreas	Pancrea
37	chr19:56189400-56193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:56189400-56193800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:56189400-56194000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr19:56189400-56194000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr19:56189400-56198000	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:56189400-56199600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:56189400-56209400	Strong transcription	Fetal Thymus	thymus
44	chr19:56189400-56209400	Strong transcription	Dnd41	blood
45	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
46	chr19:56189600-56192600	Genic enhancers	Colonic Mucosa	Colon
47	chr19:56189600-56192800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:56189600-56192800	Genic enhancers	Adipose Nuclei	Adipose
49	chr19:56189600-56192800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr19:56189600-56193600	Weak transcription	Fetal Heart	heart

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