Variant report

Variant	rs1023193
Chromosome Location	chr15:41855736-41855737
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41853242-41855924	K562	blood:	n/a	n/a
2	POLR2A	chr15:41855725-41856102	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:41854866-41856211	K562	blood:	n/a	n/a
4	POLR2A	chr15:41855023-41857639	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr15:41855642-41856303	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41853319..41856101-chr15:41857506..41859513,2	MCF-7	breast:
2	chr15:41849971..41852250-chr15:41853838..41856239,2	MCF-7	breast:
3	chr15:41853373..41858542-chr15:41950830..41955637,10	K562	blood:
4	chr15:41849459..41853162-chr15:41854225..41857161,4	MCF-7	breast:
5	chr15:41853749..41856717-chr15:41950905..41954753,5	K562	blood:
6	chr15:41854411..41856736-chr15:42132704..42135389,2	K562	blood:

No data

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000092445	Chromatin interaction
ENSG00000243708	Chromatin interaction
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1079371	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635790	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639399	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148316	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739702	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741804	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024626	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026760	0.86[AMR][1000 genomes]
rs8042535	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043421	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	esv3312256	chr15:41854897-41856388	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3312257	chr15:41854914-41856383	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1023193	LTK	cis	lung	GTEx

Chromatin state (count:90 , 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	chr15:41852600-41856800	Enhancers	HepG2	liver
6	chr15:41852600-41858600	Weak transcription	NHDF-Ad	bronchial
7	chr15:41852600-41859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:41852600-41877400	Weak transcription	HMEC	breast
9	chr15:41852800-41857600	Genic enhancers	Fetal Stomach	stomach
10	chr15:41852800-41877400	Weak transcription	NHEK	skin
11	chr15:41853000-41856000	Weak transcription	Fetal Heart	heart
12	chr15:41853000-41856400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr15:41853000-41856400	Weak transcription	Lung	lung
14	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
15	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
16	chr15:41853200-41858200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:41853200-41860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
21	chr15:41853400-41856600	Weak transcription	Right Ventricle	heart
22	chr15:41853400-41857400	Enhancers	Ovary	ovary
23	chr15:41853400-41859400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
24	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
26	chr15:41853600-41856000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:41853600-41856000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:41853600-41856200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:41853600-41857200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:41853600-41857600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
32	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:41853800-41856000	Genic enhancers	K562	blood
35	chr15:41853800-41856400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
38	chr15:41854000-41860200	Strong transcription	Dnd41	blood
39	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:41854200-41856200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:41854200-41856600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr15:41854200-41857800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr15:41854200-41859600	Weak transcription	Pancreas	Pancrea
45	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
46	chr15:41854400-41856200	Genic enhancers	Brain Germinal Matrix	brain
47	chr15:41854400-41857000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:41854400-41857600	Strong transcription	Fetal Brain Female	brain
49	chr15:41854600-41856400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
50	chr15:41854600-41856400	Genic enhancers	Brain Substantia Nigra	brain

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