Variant report

Variant	rs1725504
Chromosome Location	chr19:38546879-38546880
allele	G/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	ZNF263	chr19:38546425-38547213	HEK293-T-REx	kidney:	n/a	n/a
2	NFIC	chr19:38546259-38546984	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:38546859-38546983	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:
2	chr19:38536919..38539857-chr19:38546336..38549033,2	MCF-7	breast:
3	chr19:38546251..38550140-chr19:38563809..38566619,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221258	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10413751	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs10414433	0.82[CEU][hapmap]
rs1654349	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs1725475	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs855601	0.95[TSI][hapmap]
rs855636	0.82[CEU][hapmap]
rs855637	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1725504	ZNF180	cis	parietal	SCAN
rs1725504	ZNF404	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
4	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
6	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
7	chr19:38531400-38550800	Weak transcription	NHLF	lung
8	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
10	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
13	chr19:38539200-38548800	Weak transcription	Colonic Mucosa	Colon
14	chr19:38539200-38548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
16	chr19:38540200-38548600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:38540400-38551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:38540600-38548800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:38540600-38549000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:38540800-38548800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:38540800-38549800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:38541000-38548600	Weak transcription	Primary T cells from cord blood	blood
23	chr19:38541400-38548600	Weak transcription	GM12878-XiMat	blood
24	chr19:38543400-38553600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:38543800-38549000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:38544000-38548600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:38544200-38548200	Strong transcription	Fetal Intestine Small	intestine
29	chr19:38544600-38547200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:38545000-38547000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:38545000-38547000	Enhancers	Fetal Muscle Trunk	muscle
32	chr19:38545000-38547000	Enhancers	Fetal Thymus	thymus
33	chr19:38545000-38547200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr19:38545000-38547400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr19:38545000-38547400	Weak transcription	Aorta	Aorta
36	chr19:38545200-38547000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr19:38545200-38547000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr19:38545200-38547000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:38545200-38547200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:38545200-38547200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:38545200-38547400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr19:38545400-38547000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr19:38545400-38547000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:38545400-38547000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:38545400-38547000	Enhancers	Fetal Lung	lung
46	chr19:38545400-38547200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:38545400-38547200	Enhancers	H9 Cell Line	embryonic stem cell
48	chr19:38545400-38547200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr19:38545400-38547200	Enhancers	Fetal Kidney	kidney
50	chr19:38545400-38547200	Genic enhancers	A549	lung

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