Variant report

Variant	rs12148316
Chromosome Location	chr15:41860490-41860491
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	BRCA1	chr15:41860114-41861134	H1-hESC	embryonic stem cell:	n/a	n/a
2	HEY1	chr15:41859977-41861129	HepG2	liver:	n/a	n/a
3	TAF7	chr15:41860406-41861138	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:41860349-41860497	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:41860075-41861242	HepG2	liver:	n/a	n/a
6	SIN3A	chr15:41859944-41861076	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYBL2	chr15:41860481-41861158	HepG2	liver:	n/a	n/a
8	TEAD4	chr15:41860443-41861217	HepG2	liver:	n/a	chr15:41860914-41860923 chr15:41860783-41860792
9	HEY1	chr15:41860132-41861071	HepG2	liver:	n/a	n/a
10	GTF2F1	chr15:41859932-41861122	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXA1	chr15:41860431-41861032	HepG2	liver:	n/a	n/a
12	FOXA1	chr15:41860436-41861138	HepG2	liver:	n/a	n/a
13	ATF2	chr15:41860472-41861025	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr15:41859958-41861183	H1-hESC	embryonic stem cell:	n/a	chr15:41860244-41860254 chr15:41860245-41860254
15	RCOR1	chr15:41860426-41861219	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:41859366-41861492	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr15:41860084-41861101	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZBTB7A	chr15:41860346-41861044	HepG2	liver:	n/a	n/a
19	EP300	chr15:41860486-41861109	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:41860045-41861102	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXA1	chr15:41860481-41861156	HepG2	liver:	n/a	n/a
22	CHD1	chr15:41860335-41860894	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr15:41859950-41861404	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr15:41859978-41861269	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41849860..41852803-chr15:41858013..41860929,2	MCF-7	breast:

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1023193	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079371	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635790	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639399	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739702	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741804	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024626	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026760	0.89[AMR][1000 genomes]
rs8042535	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043421	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3391283	chr15:41859591-41860535	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3436816	chr15:41860414-41861193	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3311137	chr15:41860481-41861176	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3311138	chr15:41860481-41861176	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12148316	LTK	cis	lung	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
3	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:41852600-41877400	Weak transcription	HMEC	breast
5	chr15:41852800-41877400	Weak transcription	NHEK	skin
6	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
7	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
8	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
11	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
12	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
15	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
18	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
19	chr15:41855400-41862000	Weak transcription	NHLF	lung
20	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain
22	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:41855600-41860600	Weak transcription	NH-A	brain
25	chr15:41856400-41861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:41856800-41861400	Genic enhancers	Brain Angular Gyrus	brain
27	chr15:41857000-41860800	Weak transcription	Brain Germinal Matrix	brain
28	chr15:41857200-41860800	Weak transcription	HSMMtube	muscle
29	chr15:41857200-41862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:41857400-41864000	Genic enhancers	Brain Inferior Temporal Lobe	brain
31	chr15:41857600-41863200	Weak transcription	Fetal Brain Female	brain
32	chr15:41858200-41861000	Enhancers	Brain Substantia Nigra	brain
33	chr15:41858200-41861400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:41858600-41861000	Enhancers	A549	lung
35	chr15:41858600-41861400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:41858600-41861400	Enhancers	Fetal Heart	heart
37	chr15:41858800-41861400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:41858800-41863200	Genic enhancers	Ovary	ovary
39	chr15:41859000-41865400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:41859000-41866200	Weak transcription	NHDF-Ad	bronchial
41	chr15:41859000-41869000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:41859200-41861200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr15:41859200-41861200	Enhancers	Fetal Kidney	kidney
44	chr15:41859400-41861000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41859600-41860600	Enhancers	Adipose Nuclei	Adipose
46	chr15:41859600-41860800	Genic enhancers	Spleen	Spleen
47	chr15:41859600-41861200	Enhancers	Pancreas	Pancrea
48	chr15:41859600-41861200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:41859600-41861400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:41859600-41865800	Strong transcription	Stomach Smooth Muscle	stomach

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