Variant report

Variant	rs2412620
Chromosome Location	chr15:41829550-41829551
allele	C/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	RFX5	chr15:41829493-41829639	HepG2	liver:	n/a	chr15:41829559-41829574 chr15:41829560-41829574 chr15:41829562-41829571

No.	Distal block	Cell Line	Cell type
1	chr15:41823818..41827123-chr15:41828175..41831276,4	K562	blood:
2	chr15:41827251..41831779-chr15:41832424..41837409,12	K562	blood:
3	chr15:41814934..41817190-chr15:41828140..41829699,2	MCF-7	breast:

Variant related genes	Relation type
RPAP1	TF binding region
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070332	0.81[AMR][1000 genomes]
rs11858506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200352	0.90[EUR][1000 genomes]
rs1200353	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12442382	0.90[EUR][1000 genomes]
rs1473781	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2012453	0.86[ASN][1000 genomes]
rs2289739	0.86[YRI][hapmap]
rs2289743	0.91[JPT][hapmap]
rs2297379	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2297383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412619	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2588323	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28477443	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493004	0.83[JPT][hapmap]
rs6493005	0.83[JPT][hapmap]
rs7163686	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179280	0.89[EUR][1000 genomes]
rs9302110	0.89[EUR][1000 genomes]
rs9652441	0.96[ASN][1000 genomes]
rs9944249	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2412620	TYRO3	cis	lung	GTEx
rs2412620	LTK	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41806400-41835200	Weak transcription	Right Atrium	heart
2	chr15:41806600-41835200	Weak transcription	Fetal Heart	heart
3	chr15:41807200-41835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:41808000-41829600	Strong transcription	Fetal Stomach	stomach
5	chr15:41808600-41829600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:41808600-41835400	Weak transcription	Fetal Brain Male	brain
7	chr15:41808800-41829600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:41811600-41829600	Strong transcription	Fetal Intestine Large	intestine
9	chr15:41811600-41829800	Strong transcription	Fetal Muscle Leg	muscle
10	chr15:41811800-41829600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:41811800-41829600	Strong transcription	Brain Anterior Caudate	brain
12	chr15:41812000-41829600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:41812200-41829600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:41812200-41829600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:41812400-41829600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:41812600-41829600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:41813000-41829600	Strong transcription	Primary T cells from cord blood	blood
18	chr15:41814400-41829600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr15:41816200-41829600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:41816400-41829600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:41816600-41829600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:41818200-41829600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:41818200-41829600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:41818400-41829600	Strong transcription	Thymus	Thymus
25	chr15:41818600-41829600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:41821200-41829600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:41821200-41829600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:41821800-41835600	Weak transcription	Psoas Muscle	Psoas
29	chr15:41821800-41835800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:41822200-41835800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr15:41823000-41835600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:41823200-41835800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:41823400-41829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:41823400-41835600	Weak transcription	Small Intestine	intestine
35	chr15:41823400-41835800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:41823600-41829600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr15:41823600-41835600	Weak transcription	Stomach Mucosa	stomach
38	chr15:41823800-41829600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:41824400-41829600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:41824400-41829600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr15:41824600-41829600	Strong transcription	Fetal Brain Female	brain
42	chr15:41825000-41835200	Weak transcription	A549	lung
43	chr15:41825400-41835800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:41826600-41829800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:41826600-41835800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:41826800-41829600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:41826800-41829800	Strong transcription	NHEK	skin
48	chr15:41827600-41829600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr15:41827800-41835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:41828200-41835200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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