Variant report

Variant	rs2852151
Chromosome Location	chr18:12841176-12841177
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	CTCF	chr18:12841100-12841250	HRE	kidney:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
2	CTCF	chr18:12841147-12841284	MCF-7	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
3	CTCF	chr18:12841060-12841210	HMEC	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
4	CTCF	chr18:12841080-12841230	Caco-2	colon:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
5	SMC3	chr18:12841104-12841192	GM12878	blood:	n/a	n/a
6	CTCF	chr18:12841160-12841310	SAEC	small airway:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
7	CTCF	chr18:12841080-12841285	MCF-7	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
8	RAD21	chr18:12841066-12841292	H1-hESC	embryonic stem cell:	n/a	chr18:12841181-12841200
9	CTCF	chr18:12841160-12841310	HEEpiC	esophagus:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
10	STAT3	chr18:12840998-12841254	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr18:12841025-12841218	MCF10A-Er-Src	breast:	n/a	n/a
12	RAD21	chr18:12841078-12841321	SK-N-SH_RA	brain:	n/a	chr18:12841181-12841200
13	RAD21	chr18:12841034-12841405	H1-hESC	embryonic stem cell:	n/a	chr18:12841181-12841200
14	CTCF	chr18:12841173-12841215	ProgFib	skin:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
15	STAT3	chr18:12840995-12841207	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr18:12841040-12841190	HEEpiC	esophagus:	n/a	n/a
17	RAD21	chr18:12840988-12841437	MCF-7	breast:	n/a	chr18:12841181-12841200
18	CTCF	chr18:12841140-12841290	A549	lung:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
19	CTCF	chr18:12841091-12841288	MCF-7	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
20	CTCF	chr18:12841060-12841210	SAEC	small airway:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
21	FOS	chr18:12841116-12841200	MCF10A-Er-Src	breast:	n/a	n/a
22	CTCF	chr18:12841147-12841259	NHEK	skin:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
23	CTCF	chr18:12841040-12841190	AG04449	skin:	n/a	n/a
24	TEAD4	chr18:12841088-12841273	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr18:12841120-12841270	HMEC	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
26	CTCF	chr18:12841120-12841189	GM12878	blood:	n/a	n/a
27	CTCF	chr18:12841105-12841270	MCF-7	breast:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
28	RAD21	chr18:12841129-12841341	H1-hESC	embryonic stem cell:	n/a	chr18:12841181-12841200
29	CTCF	chr18:12841115-12841232	HepG2	liver:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
30	CTCF	chr18:12841131-12841218	SK-N-SH_RA	brain:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
31	CTCF	chr18:12841128-12841244	Hela-S3	cervix:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197
32	CTCF	chr18:12841120-12841270	RPTEC	kidney:	n/a	chr18:12841182-12841203 chr18:12841183-12841196 chr18:12841180-12841198 chr18:12841181-12841197

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	chr18:12828322..12831138-chr18:12840909..12843009,2	K562	blood:
4	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: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12957037	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12971201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2542157	0.86[GIH][hapmap]
rs2542160	0.96[GIH][hapmap]
rs2542162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847273	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847281	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847286	0.81[CEU][hapmap];0.93[GIH][hapmap]
rs3826557	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478582	0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4797709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs559406	1.00[ASN][1000 genomes]
rs588447	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs592390	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs641085	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs674222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8087237	0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.99[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2852151	PTPN2	cis	parietal	SCAN
rs2852151	FAM38B	cis	cerebellum	SCAN

Chromatin state (count:113 , 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	chr18:12838800-12842600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr18:12838800-12842800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr18:12838800-12851800	Weak transcription	Fetal Lung	lung
40	chr18:12838800-12852600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr18:12838800-12854600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr18:12838800-12855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
44	chr18:12839400-12841200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr18:12839400-12842400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:12839600-12841200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr18:12839600-12841400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr18:12839600-12841600	Enhancers	Primary B cells from peripheral blood	blood
50	chr18:12839600-12842600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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