Variant report

Variant	rs35954636
Chromosome Location	chr18:12886441-12886442
allele	G/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	SMC3	chr18:12886414-12886877	GM12878	blood:	n/a	n/a
2	CTCF	chr18:12886420-12886570	NHLF	lung:	n/a	n/a
3	CTCF	chr18:12886360-12886510	GM12872	blood:	n/a	n/a
4	CTCF	chr18:12886420-12886570	AG04450	lung:	n/a	n/a
5	POLR2A	chr18:12886257-12886457	GM12878	blood:	n/a	n/a
6	CTCF	chr18:12886400-12886550	WI-38	lung:	n/a	n/a
7	CTCF	chr18:12886288-12887074	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr18:12886378-12887005	A549	lung:	n/a	n/a
9	SPI1	chr18:12886358-12886876	HL-60	blood:	n/a	n/a
10	POLR2A	chr18:12885846-12887393	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr18:12886421-12886752	HL-60	blood:	n/a	n/a

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

Variant related genes	Relation type
PTPN2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12955302	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12963474	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12964314	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12968719	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12969241	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34153303	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34416003	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34799913	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35320197	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35923716	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967540	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71353227	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12885000-12886600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr18:12885000-12886800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr18:12885000-12887000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr18:12885000-12887400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:12885000-12888600	Weak transcription	Fetal Stomach	stomach
6	chr18:12885200-12886600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr18:12885200-12886600	Weak transcription	Gastric	stomach
8	chr18:12885200-12886800	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr18:12885200-12887400	Enhancers	Primary B cells from peripheral blood	blood
10	chr18:12885200-12887400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:12885200-12889800	Weak transcription	HSMM	muscle
12	chr18:12885200-12890600	Weak transcription	Placenta	Placenta
13	chr18:12885200-12893000	Weak transcription	Fetal Lung	lung
14	chr18:12885400-12886600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:12885400-12886800	Enhancers	Primary B cells from cord blood	blood
16	chr18:12885400-12887000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr18:12885400-12889600	Weak transcription	Hela-S3	cervix
18	chr18:12885600-12886600	Enhancers	K562	blood
19	chr18:12885600-12887200	Enhancers	Fetal Thymus	thymus
20	chr18:12885600-12893600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:12885800-12886600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr18:12885800-12886600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr18:12885800-12890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:12885800-12890600	Weak transcription	Stomach Mucosa	stomach
25	chr18:12886000-12886600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr18:12886000-12886600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr18:12886000-12886600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr18:12886000-12887000	Enhancers	GM12878-XiMat	blood
29	chr18:12886200-12886600	Weak transcription	Thymus	Thymus
30	chr18:12886200-12887000	Enhancers	HepG2	liver
31	chr18:12886200-12890200	Weak transcription	NHEK	skin
32	chr18:12886400-12886600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr18:12886400-12886800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr18:12886400-12887000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links