Variant report

Variant	rs73406791
Chromosome Location	chr18:12884894-12884895
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	MXI1	chr18:12882814-12886050	GM12878	blood:	n/a	n/a
3	NRF1	chr18:12883290-12884928	SK-N-SH	brain:	n/a	chr18:12884252-12884261 chr18:12884152-12884163 chr18:12883915-12883926 chr18:12883830-12883841 chr18:12883912-12883926 chr18:12883529-12883543 chr18:12884225-12884239 chr18:12883827-12883841 chr18:12884228-12884239 chr18:12884228-12884242 chr18:12884228-12884237 chr18:12884167-12884178 chr18:12884228-12884239 chr18:12884230-12884239
4	POLR2A	chr18:12882559-12886033	GM12891	blood:	n/a	n/a
5	POLR2A	chr18:12882859-12886028	GM12878	blood:	n/a	n/a
6	POLR2A	chr18:12884378-12886072	GM12878	blood:	n/a	n/a
7	POLR2A	chr18:12882686-12886052	GM12878	blood:	n/a	n/a
8	MAZ	chr18:12882662-12885166	IMR90	lung:	n/a	chr18:12883990-12884000 chr18:12884253-12884263 chr18:12884257-12884266
9	MXI1	chr18:12882164-12885188	SK-N-SH	brain:	n/a	n/a
10	EBF1	chr18:12883735-12886127	GM12878	blood:	n/a	chr18:12884550-12884560 chr18:12885778-12885789 chr18:12885801-12885812
11	TBL1XR1	chr18:12883670-12885115	GM12878	blood:	n/a	n/a
12	HCFC1	chr18:12882786-12885301	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr18:12881458-12885635	MCF10A-Er-Src	breast:	n/a	n/a
14	TBP	chr18:12883709-12885043	GM12878	blood:	n/a	n/a
15	MTA3	chr18:12884353-12884917	GM12878	blood:	n/a	n/a
16	CHD1	chr18:12884493-12885656	GM12878	blood:	n/a	n/a
17	MXI1	chr18:12882950-12884966	IMR90	lung:	n/a	n/a
18	CHD2	chr18:12883636-12885163	GM12878	blood:	n/a	chr18:12883985-12883995 chr18:12884250-12884260 chr18:12884158-12884168
19	POLR2A	chr18:12882565-12885987	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:65596946..65598700-chr18:12882626..12885488,2	MCF-7	breast:
2	chr18:12774117..12776643-chr18:12883699..12885836,3	K562	blood:
3	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
4	chr18:12882771..12885367-chr18:12946819..12949664,2	MCF-7	breast:
5	chr18:12760116..12762309-chr18:12883836..12885442,2	K562	blood:
6	chr18:12884698..12887915-chr18:12921814..12925737,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEH1L-5	chr18:12884514-12885555	NONHSAT058399

Variant related genes	Relation type
PTPN2	TF binding region
ENSG00000201466	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000260302	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs61054422	0.88[AFR][1000 genomes]
rs61631456	0.88[AFR][1000 genomes]
rs73406780	0.88[AFR][1000 genomes]
rs73406784	0.88[AFR][1000 genomes]
rs73406789	1.00[AFR][1000 genomes]
rs73406790	1.00[AFR][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	esv3433183	chr18:12883052-12885400	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12882200-12885000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr18:12882200-12885000	Active TSS	A549	lung
3	chr18:12882200-12885000	Active TSS	HMEC	breast
4	chr18:12882200-12885000	Active TSS	NHLF	lung
5	chr18:12882400-12885000	Active TSS	GM12878-XiMat	blood
6	chr18:12882400-12885200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr18:12882400-12885600	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr18:12882600-12885000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr18:12882600-12885000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr18:12882600-12885000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:12882600-12885000	Active TSS	Fetal Stomach	stomach
12	chr18:12882600-12885000	Active TSS	NHDF-Ad	bronchial
13	chr18:12882800-12885000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr18:12882800-12885000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:12882800-12885000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:12882800-12885000	Active TSS	Fetal Intestine Small	intestine
17	chr18:12882800-12885000	Active TSS	Placenta	Placenta
18	chr18:12882800-12885200	Active TSS	Colonic Mucosa	Colon
19	chr18:12883000-12885000	Active TSS	Aorta	Aorta
20	chr18:12883000-12885000	Active TSS	Fetal Intestine Large	intestine
21	chr18:12883000-12885000	Active TSS	Right Ventricle	heart
22	chr18:12883200-12885000	Active TSS	Brain Cingulate Gyrus	brain
23	chr18:12883200-12885000	Active TSS	Brain Hippocampus Middle	brain
24	chr18:12883200-12885000	Active TSS	Brain Substantia Nigra	brain
25	chr18:12883200-12885000	Active TSS	Duodenum Mucosa	Duodenum
26	chr18:12883200-12885000	Active TSS	Placenta Amnion	Placenta Amnion
27	chr18:12883200-12885000	Active TSS	Stomach Smooth Muscle	stomach
28	chr18:12883200-12885000	Active TSS	Hela-S3	cervix
29	chr18:12883200-12885000	Active TSS	HSMMtube	muscle
30	chr18:12883200-12885200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:12883200-12885200	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr18:12883200-12885200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr18:12883200-12885600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr18:12883400-12885000	Active TSS	Fetal Muscle Trunk	muscle
35	chr18:12883400-12885000	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr18:12883400-12885000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr18:12883400-12885200	Active TSS	Rectal Smooth Muscle	rectum
38	chr18:12883600-12885000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr18:12883800-12885000	Active TSS	Fetal Brain Male	brain
40	chr18:12883800-12885400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr18:12884400-12885000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr18:12884400-12885000	Flanking Active TSS	Dnd41	blood
43	chr18:12884600-12885000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr18:12884600-12885000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr18:12884600-12885000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr18:12884600-12885000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr18:12884600-12885000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr18:12884600-12885000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr18:12884600-12885000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr18:12884600-12885000	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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