Variant report

Variant	rs4808897
Chromosome Location	chr19:19105259-19105260
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	POLR2A	chr19:19104506-19105785	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:19105234-19105312	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:19105004-19105636	K562	blood:	n/a	n/a
4	POLR2A	chr19:19104289-19106900	K562	blood:	n/a	n/a
5	POLR2A	chr19:19105202-19105683	K562	blood:	n/a	n/a
6	POLR2A	chr19:19105095-19105326	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:19105047-19105761	K562	blood:	n/a	n/a
8	POLR2A	chr19:19105253-19105430	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:
2	chr19:19080045..19082039-chr19:19105020..19106814,2	MCF-7	breast:
3	chr19:19104797..19106786-chr19:19215223..19218180,2	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000269131	Chromatin interaction
ENSG00000181035	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164302	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10221450	0.87[EUR][1000 genomes]
rs10221529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11549380	0.97[EUR][1000 genomes]
rs28498174	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808180	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs4808181	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4808896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808899	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808909	0.95[EUR][1000 genomes]
rs4808910	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs4808912	0.97[EUR][1000 genomes]
rs4808914	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs4808915	0.97[EUR][1000 genomes]
rs4808921	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4808922	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs55658345	0.97[EUR][1000 genomes]
rs55678828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56141206	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56144126	0.87[EUR][1000 genomes]
rs56159042	0.84[EUR][1000 genomes]
rs56227420	0.87[EUR][1000 genomes]
rs60489867	0.97[EUR][1000 genomes]
rs60696741	0.97[EUR][1000 genomes]
rs72993458	0.87[EUR][1000 genomes]
rs72993462	0.85[EUR][1000 genomes]
rs73004898	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73004899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73006907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73006928	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73008923	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73008928	1.00[EUR][1000 genomes]
rs73008930	1.00[EUR][1000 genomes]
rs73008934	0.98[EUR][1000 genomes]
rs73008939	1.00[EUR][1000 genomes]
rs73008945	0.97[EUR][1000 genomes]
rs73008949	0.97[EUR][1000 genomes]
rs73008958	0.97[EUR][1000 genomes]
rs73008960	0.97[EUR][1000 genomes]
rs73010908	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
3	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:19099400-19105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:19100200-19105800	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
7	chr19:19100600-19106000	Strong transcription	Fetal Intestine Large	intestine
8	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:19100800-19106400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:19100800-19106400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:19100800-19106600	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:19101000-19105600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:19101000-19105600	Strong transcription	Fetal Stomach	stomach
14	chr19:19101000-19105800	Strong transcription	Brain Hippocampus Middle	brain
15	chr19:19101000-19106400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:19101000-19106400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:19101000-19106400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:19101000-19107200	Strong transcription	Esophagus	oesophagus
19	chr19:19101000-19109400	Strong transcription	Lung	lung
20	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
22	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
23	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
24	chr19:19101200-19106000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:19101200-19106200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr19:19101200-19106400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:19101200-19106400	Strong transcription	Brain Substantia Nigra	brain
28	chr19:19101200-19108200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:19101400-19105800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:19101400-19106200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:19101400-19106200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:19101400-19106200	Strong transcription	Placenta	Placenta
42	chr19:19101400-19106200	Strong transcription	NHDF-Ad	bronchial
43	chr19:19101400-19106400	Strong transcription	Osteobl	bone
44	chr19:19101400-19106800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:19101400-19109800	Strong transcription	Liver	Liver
46	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr19:19101600-19106400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:19101600-19106800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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