Variant report

Variant	rs7260582
Chromosome Location	chr19:52646375-52646376
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	ATF1	chr19:52646243-52646379	K562	blood:	n/a	n/a
2	ZBTB33	chr19:52646145-52646585	K562	blood:	n/a	n/a
3	POLR2A	chr19:52646155-52646452	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:52646170-52646379	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF1	chr19:52646120-52646442	H1-hESC	embryonic stem cell:	n/a	n/a
6	HEY1	chr19:52646149-52646461	K562	blood:	n/a	n/a
7	POLR2A	chr19:52646151-52646443	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:52646162-52646427	GM12878	blood:	n/a	n/a
9	SPI1	chr19:52646142-52646375	K562	blood:	n/a	chr19:52646242-52646255 chr19:52646241-52646254
10	HEY1	chr19:52646148-52646388	K562	blood:	n/a	n/a
11	POLR2A	chr19:52646143-52646453	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:52646159-52646452	H1-hESC	embryonic stem cell:	n/a	n/a
13	CBX3	chr19:52646143-52646456	K562	blood:	n/a	n/a
14	POLR2A	chr19:52646306-52646429	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:52646111-52646477	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:52646177-52646425	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELF1	chr19:52646049-52646442	K562	blood:	n/a	chr19:52646241-52646254 chr19:52646258-52646271
18	TAF1	chr19:52646134-52646387	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:52646060-52646542	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:52646054-52646470	GM12892	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP2R1A-2	chr19:52646296-52646589	NONHSAT067520

Variant related genes	Relation type
ZNF616	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12979198	0.90[ASN][1000 genomes]
rs34513092	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35591962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35729903	0.82[EUR][1000 genomes]
rs36062034	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv960860	chr19:52643619-52646538	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52644000-52647200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:52644000-52650200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:52644000-52658000	Weak transcription	Fetal Kidney	kidney
4	chr19:52644000-52658400	Weak transcription	Brain Substantia Nigra	brain
5	chr19:52644000-52658800	Weak transcription	Right Ventricle	heart
6	chr19:52644200-52656800	Weak transcription	Brain Germinal Matrix	brain
7	chr19:52644200-52658200	Weak transcription	Right Atrium	heart
8	chr19:52644400-52657800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr19:52644400-52658000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:52644600-52656800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:52645200-52647400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:52645200-52659400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:52645600-52646600	ZNF genes & repeats	Liver	Liver
14	chr19:52645800-52646400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:52645800-52646400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:52646000-52646400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:52646000-52646600	ZNF genes & repeats	NHEK	skin
18	chr19:52646200-52646400	ZNF genes & repeats	Thymus	Thymus
19	chr19:52646200-52646600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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