Variant report

Variant	rs2571104
Chromosome Location	chr19:44840789-44840790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44832482..44835383-chr19:44840174..44844169,3	MCF-7	breast:
2	chr19:44840012..44842382-chr19:44842784..44845287,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1233428	0.91[ASN][1000 genomes]
rs1233441	0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1233444	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1233447	0.86[ASN][1000 genomes]
rs1233448	0.86[ASN][1000 genomes]
rs1233459	0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1233466	0.86[ASN][1000 genomes]
rs1233467	0.86[ASN][1000 genomes]
rs1233468	0.84[ASN][1000 genomes]
rs1233470	0.88[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12974099	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434574	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1582	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1808735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1821459	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571062	0.96[ASN][1000 genomes]
rs2571099	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571101	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2571102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2609874	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2609875	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2609877	0.92[ASN][1000 genomes]
rs2609880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609881	0.86[YRI][hapmap]
rs2609892	0.86[YRI][hapmap]
rs2609894	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2609895	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609896	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609897	0.97[ASN][1000 genomes]
rs2609908	0.92[ASN][1000 genomes]
rs2722714	0.94[ASN][1000 genomes]
rs2722720	0.94[ASN][1000 genomes]
rs2722722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722726	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722727	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722731	1.00[ASN][1000 genomes]
rs2722737	0.96[ASN][1000 genomes]
rs2722751	0.92[ASN][1000 genomes]
rs4280359	1.00[ASN][1000 genomes]
rs4325673	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4640292	0.97[ASN][1000 genomes]
rs7249559	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs892595	0.82[AMR][1000 genomes];1.00[ASN][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	esv3382907	chr19:44840612-44842610	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv912110	chr19:44840789-44902190	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2571104	PTOV1	cis	parietal	SCAN
rs2571104	PTH2	cis	parietal	SCAN
rs2571104	PTOV1	cis	cerebellum	SCAN
rs2571104	LHB	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44823200-44856200	ZNF genes & repeats	Liver	Liver
2	chr19:44824800-44841000	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44825000-44846600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:44828000-44845000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
5	chr19:44828400-44846400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
6	chr19:44828600-44844200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:44828600-44845600	ZNF genes & repeats	Fetal Lung	lung
8	chr19:44828600-44848800	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:44828600-44851000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr19:44828800-44842600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:44828800-44846200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:44828800-44846400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:44829000-44844000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:44829200-44841200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:44830400-44845000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:44830600-44841200	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:44830600-44845200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr19:44830800-44840800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
19	chr19:44830800-44845600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:44830800-44850400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:44831600-44841200	ZNF genes & repeats	Aorta	Aorta
22	chr19:44831600-44841400	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr19:44831600-44846600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:44831800-44841200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:44831800-44845000	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr19:44831800-44846400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:44832000-44845600	Weak transcription	Hela-S3	cervix
28	chr19:44832000-44848200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:44832400-44841200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
30	chr19:44834800-44841200	ZNF genes & repeats	A549	lung
31	chr19:44835000-44841200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
32	chr19:44835800-44841000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
33	chr19:44836000-44841200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:44837000-44841000	ZNF genes & repeats	Fetal Heart	heart
35	chr19:44837200-44840800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
36	chr19:44837200-44841000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
37	chr19:44837200-44841200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:44837400-44841000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
39	chr19:44837400-44841200	Strong transcription	Right Ventricle	heart
40	chr19:44837400-44841200	ZNF genes & repeats	Small Intestine	intestine
41	chr19:44837400-44841400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:44837400-44841400	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr19:44837400-44841400	ZNF genes & repeats	Pancreas	Pancrea
44	chr19:44837400-44844800	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr19:44837400-44845200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr19:44837400-44851000	ZNF genes & repeats	Ovary	ovary
47	chr19:44838000-44841600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:44838400-44841200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
49	chr19:44838600-44840800	ZNF genes & repeats	Brain Angular Gyrus	brain
50	chr19:44838600-44840800	ZNF genes & repeats	Gastric	stomach

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