Variant report

Variant	rs2297383
Chromosome Location	chr15:41828571-41828572
allele	A/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	POLR2A	chr15:41828359-41828680	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:41828485-41828857	K562	blood:	n/a	n/a

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:
4	chr15:41784287..41786620-chr15:41827580..41829440,3	K562	blood:

Variant related genes	Relation type
RPAP1	TF binding region
ENSG00000137825	Chromatin interaction
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11070332	0.81[AMR][1000 genomes]
rs11858506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200352	0.91[EUR][1000 genomes]
rs1200353	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12442382	0.91[EUR][1000 genomes]
rs1473781	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012453	0.88[ASN][1000 genomes]
rs2297379	0.80[ASN][1000 genomes]
rs2412619	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2588323	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28477443	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163686	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7179280	0.87[EUR][1000 genomes]
rs9302110	0.90[EUR][1000 genomes]
rs9652441	0.94[ASN][1000 genomes]

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
rs2297383	LTK	cis	lung	GTEx
rs2297383	TYRO3	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	chr15:41808600-41829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:41808600-41829600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:41808600-41835400	Weak transcription	Fetal Brain Male	brain
8	chr15:41808800-41829600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:41809000-41829400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:41809000-41829400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:41809600-41829200	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:41809600-41829400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:41811600-41829600	Strong transcription	Fetal Intestine Large	intestine
14	chr15:41811600-41829800	Strong transcription	Fetal Muscle Leg	muscle
15	chr15:41811800-41829400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41811800-41829400	Strong transcription	Brain Hippocampus Middle	brain
17	chr15:41811800-41829400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr15:41811800-41829600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:41811800-41829600	Strong transcription	Brain Anterior Caudate	brain
20	chr15:41812000-41829600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:41812200-41828800	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr15:41812200-41829200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr15:41812200-41829600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:41812200-41829600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:41812400-41829200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:41812400-41829400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:41812400-41829400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:41812400-41829400	Strong transcription	Liver	Liver
29	chr15:41812400-41829400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:41812400-41829400	Strong transcription	Fetal Intestine Small	intestine
31	chr15:41812400-41829400	Strong transcription	Left Ventricle	heart
32	chr15:41812400-41829600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:41812600-41829400	Strong transcription	Brain Germinal Matrix	brain
34	chr15:41812600-41829400	Strong transcription	Pancreas	Pancrea
35	chr15:41812600-41829600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:41812800-41828800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:41813000-41829600	Strong transcription	Primary T cells from cord blood	blood
38	chr15:41814400-41829600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr15:41815000-41829400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:41815400-41829000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:41815800-41829200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:41815800-41829400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:41816200-41829600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:41816400-41828800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr15:41816400-41829600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:41816600-41828800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:41816600-41829600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:41818200-41829400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr15:41818200-41829400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:41818200-41829600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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