Variant report

Variant	rs7227207
Chromosome Location	chr18:12819616-12819617
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	RUNX3	chr18:12819239-12820158	GM12878	blood:	n/a	n/a
2	SMC3	chr18:12819419-12819619	GM12878	blood:	n/a	n/a
3	RUNX3	chr18:12819330-12819738	GM12878	blood:	n/a	n/a
4	BATF	chr18:12819379-12819642	GM12878	blood:	n/a	n/a
5	BHLHE40	chr18:12819416-12819644	GM12878	blood:	n/a	n/a
6	PBX3	chr18:12819463-12819631	GM12878	blood:	n/a	n/a
7	TCF12	chr18:12819409-12819643	GM12878	blood:	n/a	n/a
8	ATF2	chr18:12819281-12819786	GM12878	blood:	n/a	n/a
9	TCF12	chr18:12819382-12819632	GM12878	blood:	n/a	n/a
10	MXI1	chr18:12819407-12819616	GM12878	blood:	n/a	n/a
11	EP300	chr18:12819412-12819639	GM12878	blood:	n/a	n/a
12	BATF	chr18:12819359-12819665	GM12878	blood:	n/a	n/a
13	JUN	chr18:12819560-12819711	H1-hESC	embryonic stem cell:	n/a	n/a
14	NFIC	chr18:12819264-12819669	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12817654..12819738-chr18:12836432..12839410,2	K562	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10502416	0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11080605	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11080606	0.91[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs12607710	0.86[JPT][hapmap]
rs16939910	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3737361	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3786158	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62097819	0.85[ASN][1000 genomes]
rs62097820	0.87[ASN][1000 genomes]
rs62097858	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7242788	0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8091720	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	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
8	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
3	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
4	chr18:12790200-12828000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr18:12790600-12820000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
7	chr18:12791600-12828000	Weak transcription	HUVEC	blood vessel
8	chr18:12791800-12821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr18:12797800-12819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr18:12806400-12827600	Strong transcription	Dnd41	blood
12	chr18:12806800-12827400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr18:12807200-12826600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
15	chr18:12807400-12821400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:12808600-12827400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr18:12808800-12827200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr18:12809000-12828000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr18:12809000-12828000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr18:12809400-12819800	Weak transcription	Brain Hippocampus Middle	brain
21	chr18:12809600-12824600	Weak transcription	Esophagus	oesophagus
22	chr18:12809600-12825200	Weak transcription	Aorta	Aorta
23	chr18:12809600-12828000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:12809600-12833200	Weak transcription	HSMM	muscle
25	chr18:12809600-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:12809600-12838200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr18:12811200-12821800	Weak transcription	Stomach Mucosa	stomach
28	chr18:12811600-12828000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr18:12811800-12827400	Weak transcription	Psoas Muscle	Psoas
30	chr18:12812000-12838400	Weak transcription	Right Ventricle	heart
31	chr18:12812600-12822600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:12812800-12819800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr18:12814400-12824400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr18:12814600-12824000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr18:12814600-12828200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr18:12814600-12828200	Weak transcription	A549	lung
38	chr18:12815000-12822600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr18:12815000-12824200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr18:12815400-12827200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr18:12815800-12820000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:12816200-12824200	Weak transcription	Fetal Kidney	kidney
43	chr18:12816200-12828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr18:12816400-12819800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:12816400-12820000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr18:12816400-12820000	Weak transcription	Fetal Muscle Leg	muscle
47	chr18:12816400-12821600	Weak transcription	Spleen	Spleen
48	chr18:12816400-12824200	Weak transcription	Gastric	stomach
49	chr18:12816400-12824200	Weak transcription	Pancreas	Pancrea
50	chr18:12816400-12824200	Weak transcription	Hela-S3	cervix

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