Variant report

Variant	rs11639399
Chromosome Location	chr15:41857216-41857217
allele	A/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	POLR2A	chr15:41856390-41857223	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr15:41856229-41857524	K562	blood:	n/a	n/a
3	REST	chr15:41856176-41857362	H1-neurons	neurons:	n/a	chr15:41856892-41856905 chr15:41857166-41857184 chr15:41856895-41856908
4	CCNT2	chr15:41857032-41857519	K562	blood:	n/a	n/a
5	POLR2A	chr15:41856706-41857290	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:41856429-41857237	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr15:41857143-41857561	K562	blood:	n/a	n/a
8	POLR2A	chr15:41855023-41857639	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr15:41856338-41857405	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:41856102-41857580	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:41857195-41857245	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41856836..41858542-chr15:41952173..41953837,2	K562	blood:
2	chr15:41853373..41858542-chr15:41950830..41955637,10	K562	blood:

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1023193	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079371	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635790	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148316	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024626	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026760	0.89[AMR][1000 genomes]
rs8042535	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043421	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	esv3359172	chr15:41856320-41857334	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11639399	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	chr15:41852400-41859600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
4	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:41852600-41858600	Weak transcription	NHDF-Ad	bronchial
6	chr15:41852600-41859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:41852600-41877400	Weak transcription	HMEC	breast
8	chr15:41852800-41857600	Genic enhancers	Fetal Stomach	stomach
9	chr15:41852800-41877400	Weak transcription	NHEK	skin
10	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
11	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
12	chr15:41853200-41858200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41853200-41860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
17	chr15:41853400-41857400	Enhancers	Ovary	ovary
18	chr15:41853400-41859400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
19	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
21	chr15:41853600-41857600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
22	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
23	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
27	chr15:41854000-41860200	Strong transcription	Dnd41	blood
28	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:41854200-41857800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:41854200-41859600	Weak transcription	Pancreas	Pancrea
32	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
33	chr15:41854400-41857600	Strong transcription	Fetal Brain Female	brain
34	chr15:41854800-41857400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr15:41855000-41857400	Genic enhancers	Fetal Lung	lung
36	chr15:41855000-41858200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
38	chr15:41855200-41857400	Enhancers	Spleen	Spleen
39	chr15:41855200-41858000	Enhancers	Fetal Kidney	kidney
40	chr15:41855200-41858000	Weak transcription	A549	lung
41	chr15:41855200-41860000	Weak transcription	Gastric	stomach
42	chr15:41855400-41857400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41855400-41857400	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr15:41855400-41857600	Enhancers	Placenta	Placenta
45	chr15:41855400-41860200	Weak transcription	Esophagus	oesophagus
46	chr15:41855400-41862000	Weak transcription	NHLF	lung
47	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain
49	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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