Variant report

Variant	rs2542173
Chromosome Location	chr18:12700092-12700093
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	FOSL2	chr18:12699813-12700145	HepG2	liver:	n/a	n/a
2	FOXA1	chr18:12699727-12700114	HepG2	liver:	n/a	chr18:12699992-12700007
3	FOXA1	chr18:12699751-12700259	HepG2	liver:	n/a	chr18:12699992-12700007
4	FOXA1	chr18:12699690-12700272	HepG2	liver:	n/a	chr18:12699992-12700007
5	FOSL2	chr18:12699839-12700093	HepG2	liver:	n/a	n/a
6	FOXA2	chr18:12699754-12700561	HepG2	liver:	n/a	n/a
7	ARID3A	chr18:12699731-12700601	HepG2	liver:	n/a	n/a
8	NFIC	chr18:12699712-12700191	HepG2	liver:	n/a	n/a
9	FOXA2	chr18:12699770-12700126	HepG2	liver:	n/a	n/a
10	EP300	chr18:12699702-12700199	HepG2	liver:	n/a	n/a
11	CEBPB	chr18:12699729-12700587	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12677577..12680065-chr18:12699898..12703044,3	K562	blood:
2	chr18:12699667..12702594-chr18:12881299..12884281,3	K562	blood:
3	chr18:12689483..12696263-chr18:12698961..12704404,9	MCF-7	breast:
4	chr18:12698612..12700197-chr18:12928649..12930507,2	K562	blood:
5	chr18:12406252..12409116-chr18:12699672..12701773,2	MCF-7	breast:
6	chr18:12685127..12688617-chr18:12697968..12702228,5	MCF-7	breast:

Variant related genes	Relation type
PSMG2	TF binding region
CEP76	TF binding region
ENSG00000101624	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000141391	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10468685	1.00[EUR][1000 genomes]
rs1116261	1.00[EUR][1000 genomes]
rs13381820	1.00[EUR][1000 genomes]
rs16939851	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16939913	1.00[EUR][1000 genomes]
rs1785314	1.00[EUR][1000 genomes]
rs28436108	1.00[EUR][1000 genomes]
rs2847263	1.00[EUR][1000 genomes]
rs2847264	1.00[EUR][1000 genomes]
rs34609495	1.00[EUR][1000 genomes]
rs559719	1.00[EUR][1000 genomes]
rs59434054	1.00[EUR][1000 genomes]
rs61320647	1.00[EUR][1000 genomes]
rs7236539	1.00[EUR][1000 genomes]
rs7240157	1.00[EUR][1000 genomes]
rs8087452	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs908577	1.00[TSI][hapmap]
rs9951546	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12658800-12701800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr18:12659000-12700200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12660400-12700800	Weak transcription	Fetal Brain Male	brain
4	chr18:12662800-12701600	Weak transcription	Aorta	Aorta
5	chr18:12667000-12701600	Weak transcription	Gastric	stomach
6	chr18:12672200-12701400	Weak transcription	Colonic Mucosa	Colon
7	chr18:12673200-12701600	Weak transcription	Psoas Muscle	Psoas
8	chr18:12674600-12701600	Weak transcription	Right Ventricle	heart
9	chr18:12674600-12701600	Weak transcription	Small Intestine	intestine
10	chr18:12674800-12700600	Weak transcription	Brain Substantia Nigra	brain
11	chr18:12674800-12701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr18:12678200-12701400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr18:12678400-12701200	Weak transcription	NH-A	brain
14	chr18:12678400-12701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:12678400-12701600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:12678400-12701600	Weak transcription	HSMMtube	muscle
17	chr18:12679600-12700400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr18:12679600-12700400	Weak transcription	Colon Smooth Muscle	Colon
19	chr18:12679600-12700600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr18:12679600-12701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:12679600-12701000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr18:12679600-12701200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr18:12679600-12701600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:12679800-12701000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr18:12679800-12701000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr18:12679800-12701000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr18:12680000-12701200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr18:12680000-12701600	Weak transcription	Esophagus	oesophagus
29	chr18:12680000-12701600	Weak transcription	Ovary	ovary
30	chr18:12680200-12700800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr18:12680800-12701400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr18:12684800-12701600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr18:12685200-12701600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:12685400-12701400	Weak transcription	Fetal Intestine Small	intestine
35	chr18:12685600-12701400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:12686400-12701000	Weak transcription	Brain Hippocampus Middle	brain
37	chr18:12686800-12700800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr18:12686800-12701600	Weak transcription	Lung	lung
39	chr18:12687200-12701000	Weak transcription	Primary B cells from cord blood	blood
40	chr18:12687200-12701200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr18:12687400-12701000	Weak transcription	Fetal Lung	lung
42	chr18:12688400-12701400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:12690600-12701000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr18:12691000-12700800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr18:12692400-12700400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr18:12692600-12700800	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr18:12692600-12701400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr18:12693000-12701000	Weak transcription	Brain Germinal Matrix	brain
49	chr18:12693800-12701000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr18:12694000-12700400	Strong transcription	Primary T cells fromperipheralblood	blood

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