Variant report

Variant	rs142909392
Chromosome Location	chr18:12885568-12885569
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	POLR2A	chr18:12882099-12885668	MCF10A-Er-Src	breast:	n/a	n/a
2	TBP	chr18:12885257-12885999	GM12878	blood:	n/a	n/a
3	CCNT2	chr18:12885423-12885668	K562	blood:	n/a	chr18:12885541-12885561
4	MXI1	chr18:12882814-12886050	GM12878	blood:	n/a	n/a
5	POLR2A	chr18:12882559-12886033	GM12891	blood:	n/a	n/a
6	ARID3A	chr18:12885459-12885677	K562	blood:	n/a	n/a
7	TEAD4	chr18:12885315-12885750	K562	blood:	n/a	n/a
8	POLR2A	chr18:12882859-12886028	GM12878	blood:	n/a	n/a
9	POU2F2	chr18:12885510-12885785	GM12878	blood:	n/a	chr18:12885626-12885639
10	GATA1	chr18:12885074-12885746	PBDE	blood:	n/a	chr18:12885544-12885561
11	EP300	chr18:12885400-12885746	K562	blood:	n/a	n/a
12	POLR2A	chr18:12884378-12886072	GM12878	blood:	n/a	n/a
13	POLR2A	chr18:12882686-12886052	GM12878	blood:	n/a	n/a
14	POLR2A	chr18:12885282-12885654	HepG2	liver:	n/a	n/a
15	EBF1	chr18:12883735-12886127	GM12878	blood:	n/a	chr18:12884550-12884560 chr18:12885778-12885789 chr18:12885801-12885812
16	ATF2	chr18:12885496-12885957	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr18:12885405-12885712	K562	blood:	n/a	n/a
18	GTF2F1	chr18:12885492-12885686	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr18:12885288-12885846	H1-hESC	embryonic stem cell:	n/a	n/a
20	NANOG	chr18:12885496-12885881	H1-hESC	embryonic stem cell:	n/a	n/a
21	POU2F2	chr18:12885471-12885882	GM12891	blood:	n/a	chr18:12885626-12885639
22	POLR2A	chr18:12885519-12885771	Raji	blood:	n/a	n/a
23	RUNX3	chr18:12885447-12885913	GM12878	blood:	n/a	n/a
24	POLR2A	chr18:12885514-12885716	GM12878	blood:	n/a	n/a
25	POU2F2	chr18:12885450-12885929	GM12878	blood:	n/a	chr18:12885626-12885639
26	RCOR1	chr18:12885378-12885997	GM12878	blood:	n/a	n/a
27	POU5F1	chr18:12885465-12886009	H1-hESC	embryonic stem cell:	n/a	chr18:12885626-12885639
28	MYC	chr18:12885466-12885705	K562	blood:	n/a	n/a
29	MTA3	chr18:12885378-12886006	GM12878	blood:	n/a	n/a
30	POLR2A	chr18:12885349-12885917	GM12892	blood:	n/a	n/a
31	ATF2	chr18:12885468-12886010	GM12878	blood:	n/a	n/a
32	BHLHE40	chr18:12885061-12885968	GM12878	blood:	n/a	n/a
33	MAFK	chr18:12885527-12885727	K562	blood:	n/a	n/a
34	JUND	chr18:12885522-12885901	H1-hESC	embryonic stem cell:	n/a	n/a
35	CEBPD	chr18:12885350-12885779	K562	blood:	n/a	n/a
36	POLR2A	chr18:12885398-12885794	GM12892	blood:	n/a	n/a
37	IRF1	chr18:12885439-12885823	K562	blood:	n/a	n/a
38	EP300	chr18:12885322-12885944	GM12878	blood:	n/a	n/a
39	WRNIP1	chr18:12885412-12885969	GM12878	blood:	n/a	n/a
40	POLR2A	chr18:12881458-12885635	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr18:12885366-12885857	GM12878	blood:	n/a	n/a
42	ZMIZ1	chr18:12885386-12885707	K562	blood:	n/a	n/a
43	RCOR1	chr18:12885368-12885840	K562	blood:	n/a	n/a
44	MAX	chr18:12885520-12885807	H1-hESC	embryonic stem cell:	n/a	n/a
45	EBF1	chr18:12885526-12886008	GM12878	blood:	n/a	chr18:12885778-12885789 chr18:12885801-12885812
46	POU2F2	chr18:12885307-12886057	GM12878	blood:	n/a	chr18:12885626-12885639
47	CHD1	chr18:12884493-12885656	GM12878	blood:	n/a	n/a
48	JUND	chr18:12885487-12885723	K562	blood:	n/a	n/a
49	EBF1	chr18:12885472-12886051	GM12878	blood:	n/a	chr18:12885778-12885789 chr18:12885801-12885812
50	ELF1	chr18:12885421-12885781	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
2	chr18:12885210..12887915-chr18:12922240..12924261,2	K562	blood:
3	chr18:12884698..12887915-chr18:12921814..12925737,3	K562	blood:

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000260302	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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	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
3	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
4	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
5	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
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a
7	nsv132152	chr18:12885273-12890021	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12882400-12885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr18:12883200-12885600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr18:12884600-12885600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr18:12884600-12885600	Flanking Active TSS	Fetal Thymus	thymus
5	chr18:12884600-12885800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr18:12884800-12885600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr18:12884800-12885600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr18:12884800-12885600	Weak transcription	Psoas Muscle	Psoas
9	chr18:12884800-12885600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr18:12884800-12885600	Flanking Active TSS	K562	blood
11	chr18:12884800-12886000	Enhancers	Small Intestine	intestine
12	chr18:12884800-12886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr18:12885000-12885600	Enhancers	Primary T cells from cord blood	blood
14	chr18:12885000-12885600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr18:12885000-12885600	Enhancers	Brain Angular Gyrus	brain
16	chr18:12885000-12885600	Enhancers	Dnd41	blood
17	chr18:12885000-12885800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr18:12885000-12885800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:12885000-12885800	Enhancers	Stomach Mucosa	stomach
20	chr18:12885000-12885800	Enhancers	HepG2	liver
21	chr18:12885000-12886000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:12885000-12886000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr18:12885000-12886000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr18:12885000-12886000	Flanking Active TSS	GM12878-XiMat	blood
25	chr18:12885000-12886600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr18:12885000-12886800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr18:12885000-12887000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr18:12885000-12887400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:12885000-12888600	Weak transcription	Fetal Stomach	stomach
30	chr18:12885200-12885600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr18:12885200-12885600	Enhancers	Duodenum Mucosa	Duodenum
32	chr18:12885200-12885600	Enhancers	Fetal Intestine Small	intestine
33	chr18:12885200-12885600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr18:12885200-12885800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:12885200-12885800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr18:12885200-12885800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:12885200-12885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr18:12885200-12885800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr18:12885200-12886000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr18:12885200-12886400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr18:12885200-12886400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr18:12885200-12886600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr18:12885200-12886600	Weak transcription	Gastric	stomach
44	chr18:12885200-12886800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr18:12885200-12887400	Enhancers	Primary B cells from peripheral blood	blood
46	chr18:12885200-12887400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr18:12885200-12889800	Weak transcription	HSMM	muscle
48	chr18:12885200-12890600	Weak transcription	Placenta	Placenta
49	chr18:12885200-12893000	Weak transcription	Fetal Lung	lung
50	chr18:12885400-12885600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links