Variant report

Variant	rs17657106
Chromosome Location	chr18:12840879-12840880
allele	C/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	USF2	chr18:12840763-12840898	GM12878	blood:	n/a	n/a
2	MAFK	chr18:12840619-12840968	HepG2	liver:	n/a	n/a
3	CTCF	chr18:12840820-12840970	HEEpiC	esophagus:	n/a	n/a
4	MAFK	chr18:12840642-12840943	IMR90	lung:	n/a	n/a
5	EP300	chr18:12838996-12840925	GM12878	blood:	n/a	chr18:12840436-12840446 chr18:12839731-12839745
6	MAFF	chr18:12840661-12840965	HepG2	liver:	n/a	n/a
7	MAFK	chr18:12840632-12840964	HepG2	liver:	n/a	n/a
8	ZNF384	chr18:12838418-12840916	GM12878	blood:	n/a	n/a
9	MAFK	chr18:12840620-12840929	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12836859..12842714-chr18:12880630..12885724,12	MCF-7	breast:
2	chr18:12838410..12841239-chr18:12848544..12850733,2	K562	blood:
3	chr18:12838530..12843294-chr18:12882526..12884530,4	MCF-7	breast:

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10502414	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs10502415	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs1065630	0.83[EUR][1000 genomes]
rs16939859	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs17597893	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs17598047	0.83[CEU][hapmap];0.93[EUR][1000 genomes]
rs17656120	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs17656142	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs2847288	0.81[CEU][hapmap]
rs45458596	0.84[EUR][1000 genomes]
rs45506596	0.85[EUR][1000 genomes]
rs45510799	0.85[EUR][1000 genomes]
rs45518232	0.86[EUR][1000 genomes]
rs45518540	0.85[EUR][1000 genomes]
rs45575332	0.86[EUR][1000 genomes]
rs45576131	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs45602843	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45626137	0.86[EUR][1000 genomes]
rs57450722	0.88[EUR][1000 genomes]
rs57528860	0.86[EUR][1000 genomes]
rs59368414	0.88[EUR][1000 genomes]
rs59698881	0.88[EUR][1000 genomes]
rs60617398	0.86[EUR][1000 genomes]
rs73402502	0.86[EUR][1000 genomes]
rs73404411	0.87[EUR][1000 genomes]
rs73404414	0.88[EUR][1000 genomes]
rs73404420	0.88[EUR][1000 genomes]
rs73404421	0.88[EUR][1000 genomes]
rs73404424	0.88[EUR][1000 genomes]
rs73404453	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73414061	0.84[EUR][1000 genomes]
rs8084006	0.88[EUR][1000 genomes]
rs8085163	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs8088256	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs8092305	0.86[EUR][1000 genomes]
rs973767	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
7	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
3	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:12828400-12842600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
8	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
9	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
10	chr18:12829200-12842200	Weak transcription	HUVEC	blood vessel
11	chr18:12829800-12841200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:12834200-12850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr18:12836800-12842400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr18:12837400-12841600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr18:12838000-12841600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr18:12838600-12841400	Enhancers	Pancreas	Pancrea
17	chr18:12838600-12841800	Weak transcription	Stomach Mucosa	stomach
18	chr18:12838600-12842200	Weak transcription	Placenta	Placenta
19	chr18:12838600-12842400	Weak transcription	Fetal Stomach	stomach
20	chr18:12838600-12843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr18:12838600-12843000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr18:12838600-12843000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr18:12838600-12843400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr18:12838600-12843400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr18:12838600-12843400	Weak transcription	Gastric	stomach
26	chr18:12838600-12848400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:12838600-12851800	Weak transcription	Fetal Brain Male	brain
28	chr18:12838600-12852000	Weak transcription	Ovary	ovary
29	chr18:12838600-12854000	Weak transcription	Left Ventricle	heart
30	chr18:12838600-12856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr18:12838600-12856200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:12838600-12857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr18:12838600-12862400	Weak transcription	NH-A	brain
36	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:12838800-12841000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr18:12838800-12841000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr18:12838800-12842600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr18:12838800-12842800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr18:12838800-12851800	Weak transcription	Fetal Lung	lung
42	chr18:12838800-12852600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:12838800-12854600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr18:12838800-12855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
46	chr18:12839200-12841000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr18:12839200-12841000	Enhancers	Small Intestine	intestine
48	chr18:12839400-12841000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr18:12839400-12841200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr18:12839400-12842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links