Variant report

Variant	rs8104242
Chromosome Location	chr19:56190815-56190816
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	chr19:56190664-56191182	K562	blood:	n/a	n/a
2	POLR2A	chr19:56190743-56190991	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:56190712-56191542	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:56190389-56191148	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:56190379-56191730	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:56190537-56191118	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56189741..56193540-chr19:56204383..56209311,7	K562	blood:
3	chr19:56172318..56174905-chr19:56187838..56190897,3	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000267523	TF binding region
ENSG00000203305	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000267183	Chromatin interaction
ENSG00000267117	Chromatin interaction
ENSG00000267018	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10402618	0.87[ASN][1000 genomes]
rs10403866	0.93[ASN][1000 genomes]
rs10408613	0.90[ASN][1000 genomes]
rs10410404	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.86[ASN][1000 genomes]
rs10410802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10410886	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10412050	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10415521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417539	0.95[ASN][1000 genomes]
rs10421319	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11882031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287791	0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap]
rs28385383	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28595590	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28668166	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs310437	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs310441	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs523509	0.84[ASN][1000 genomes]
rs575274	0.88[JPT][hapmap]
rs57544196	0.95[ASN][1000 genomes]
rs584405	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60873246	0.91[ASN][1000 genomes]
rs610811	0.81[JPT][hapmap]
rs617073	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs648651	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs681804	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256441	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73613281	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8100143	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109983	0.96[ASN][1000 genomes]

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	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
8	nsv522559	chr19:56185250-56190815	Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8104242	ZNF580	cis	lymphoblastoid	seeQTL

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	chr19:56188200-56192200	Genic enhancers	Esophagus	oesophagus
4	chr19:56188200-56192800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:56188400-56191600	Genic enhancers	Lung	lung
7	chr19:56188400-56192000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:56188400-56192200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr19:56188400-56193200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:56188400-56193800	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:56188400-56194000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:56188600-56192800	Genic enhancers	Gastric	stomach
16	chr19:56188600-56193000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:56188600-56194000	Strong transcription	A549	lung
18	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
21	chr19:56188800-56191000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:56188800-56192800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:56188800-56194000	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
25	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
26	chr19:56189000-56191000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:56189000-56192200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr19:56189000-56192600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr19:56189000-56193400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:56189000-56193400	Genic enhancers	Spleen	Spleen
31	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
32	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
33	chr19:56189200-56193200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr19:56189200-56193400	Genic enhancers	Stomach Mucosa	stomach
35	chr19:56189200-56195200	Genic enhancers	Fetal Intestine Small	intestine
36	chr19:56189200-56195400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:56189200-56199400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:56189400-56191600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:56189400-56192000	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr19:56189400-56192200	Weak transcription	Psoas Muscle	Psoas
43	chr19:56189400-56192400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:56189400-56192400	Genic enhancers	Right Ventricle	heart
45	chr19:56189400-56192600	Strong transcription	Aorta	Aorta
46	chr19:56189400-56192600	Genic enhancers	Pancreas	Pancrea
47	chr19:56189400-56193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:56189400-56193800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:56189400-56194000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr19:56189400-56194000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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