Variant report

Variant	rs1628289
Chromosome Location	chr19:41707094-41707095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41703762..41708765-chr19:41768363..41772371,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10419231	0.80[AMR][1000 genomes]
rs168109	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1709138	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs338581	0.81[EUR][1000 genomes]
rs338585	0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs338586	0.83[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs338587	0.94[ASN][1000 genomes]
rs338589	0.91[ASN][1000 genomes]
rs338593	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs338594	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs338598	0.84[CHD][hapmap]
rs7254036	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100811	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv911767	chr19:41649516-41716271	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1628289	CADM4	cis	cerebellum	SCAN
rs1628289	QPCTL	cis	parietal	SCAN
rs1628289	PSG9	cis	parietal	SCAN
rs1628289	SERTAD3	cis	lymphoblastoid	seeQTL
rs1628289	ZNF296	cis	cerebellum	SCAN
rs1628289	AXL	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41699600-41724400	Weak transcription	Right Atrium	heart
2	chr19:41700000-41722200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:41700000-41724400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:41700200-41724200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41700600-41714600	Weak transcription	Spleen	Spleen
6	chr19:41700800-41711400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:41701200-41713800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:41701600-41713800	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr19:41701600-41714600	Strong transcription	Fetal Intestine Small	intestine
10	chr19:41701800-41711400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:41701800-41711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:41701800-41714400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:41701800-41714800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:41702000-41713800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:41702000-41722400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr19:41702200-41714000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:41702600-41711800	Weak transcription	NHEK	skin
18	chr19:41702600-41712000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:41702800-41713600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:41702800-41713800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:41703000-41714600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:41704800-41711800	Weak transcription	Stomach Mucosa	stomach
23	chr19:41704800-41712200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:41705000-41707200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:41705000-41707200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:41705000-41711800	Weak transcription	Lung	lung
27	chr19:41705000-41712000	Weak transcription	Colonic Mucosa	Colon
28	chr19:41705200-41709200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:41705200-41711400	Weak transcription	Esophagus	oesophagus
30	chr19:41705200-41712000	Weak transcription	NHLF	lung
31	chr19:41705400-41713200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:41706200-41709600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:41706400-41707400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:41706400-41710200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:41706400-41710200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:41706400-41713800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:41706600-41707200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:41706600-41707600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:41706600-41707800	Strong transcription	Gastric	stomach
40	chr19:41706600-41709600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:41706600-41710000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr19:41706600-41710400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr19:41706800-41707200	Enhancers	GM12878-XiMat	blood
44	chr19:41706800-41708400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr19:41706800-41710200	Weak transcription	HepG2	liver
46	chr19:41706800-41712000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr19:41707000-41707800	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr19:41707000-41708600	Strong transcription	A549	lung
49	chr19:41707000-41710600	Strong transcription	Fetal Stomach	stomach
50	chr19:41707000-41713800	Strong transcription	Fetal Intestine Large	intestine

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