Variant report

Variant	rs1449082
Chromosome Location	chr18:29264028-29264029
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	POLR2A	chr18:29263962-29266139	GM18951	blood:	n/a	n/a
2	PML	chr18:29263917-29266204	GM12878	blood:	n/a	n/a
3	MYC	chr18:29263890-29264060	MCF10A-Er-Src	breast:	n/a	n/a
4	RUNX3	chr18:29264025-29264486	GM12878	blood:	n/a	n/a
5	CHD1	chr18:29263679-29264362	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr18:29263952-29264846	H1-neurons	neurons:	n/a	chr18:29264801-29264814 chr18:29264809-29264822
7	E2F4	chr18:29263892-29264162	MCF10A-Er-Src	breast:	n/a	n/a
8	SIN3A	chr18:29263824-29266100	H1-hESC	embryonic stem cell:	n/a	chr18:29265439-29265452 chr18:29265145-29265158
9	KAP1	chr18:29263693-29264491	HEK293	kidney:	n/a	n/a
10	POLR2A	chr18:29264009-29266286	GM12892	blood:	n/a	n/a
11	POLR2A	chr18:29263761-29266391	GM19099	blood:	n/a	n/a
12	ATF1	chr18:29263987-29264156	K562	blood:	n/a	n/a
13	POLR2A	chr18:29263999-29266298	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr18:29263965-29264348	MCF10A-Er-Src	breast:	n/a	n/a
15	ZNF263	chr18:29263898-29265483	HEK293-T-REx	kidney:	n/a	chr18:29264726-29264735 chr18:29264745-29264754
16	POLR2A	chr18:29263986-29264539	GM12878	blood:	n/a	n/a
17	WRNIP1	chr18:29263720-29264733	GM12878	blood:	n/a	n/a
18	CHD1	chr18:29263327-29264447	GM12878	blood:	n/a	n/a
19	MTA3	chr18:29263836-29264658	GM12878	blood:	n/a	n/a
20	POLR2A	chr18:29263608-29266533	GM12878	blood:	n/a	n/a
21	POLR2A	chr18:29263972-29266236	GM12892	blood:	n/a	n/a
22	RELA	chr18:29263748-29266310	GM12891	blood:	n/a	n/a
23	NFATC1	chr18:29263954-29264449	GM12878	blood:	n/a	n/a
24	SMC3	chr18:29263982-29264135	GM12878	blood:	n/a	n/a
25	POLR2A	chr18:29263652-29266352	GM12878	blood:	n/a	n/a
26	POLR2A	chr18:29263995-29266247	GM12891	blood:	n/a	n/a
27	POLR2A	chr18:29263969-29265501	GM12891	blood:	n/a	n/a
28	POLR2A	chr18:29263662-29267464	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29235239..29238459-chr18:29263541..29266170,4	MCF-7	breast:
2	chr18:29259339..29260872-chr18:29261230..29264110,2	K562	blood:

Variant related genes	Relation type
ENSG00000259985	TF binding region
ENSG00000118276	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10048377	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10775449	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11081706	0.85[YRI][hapmap]
rs11081707	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11081708	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11660271	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11664177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12327203	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12605321	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12964693	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1551006	0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs1614197	0.97[EUR][1000 genomes]
rs17661533	1.00[YRI][hapmap]
rs1979105	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs34530749	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4799589	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs718780	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8098191	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs968325	0.84[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3344706	chr18:29263704-29266352	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1449082	CDH2	cis	cerebellum	SCAN
rs1449082	DSC1	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29253600-29264200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:29259000-29264400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr18:29260400-29264200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:29260600-29264200	Weak transcription	Left Ventricle	heart
5	chr18:29260600-29264200	Weak transcription	Lung	lung
6	chr18:29260600-29264200	Weak transcription	Pancreas	Pancrea
7	chr18:29261000-29264200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:29261000-29264200	Weak transcription	Gastric	stomach
9	chr18:29261600-29265600	Active TSS	GM12878-XiMat	blood
10	chr18:29262000-29266200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr18:29262400-29265800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr18:29262600-29264400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr18:29262600-29266400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr18:29262800-29264400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr18:29262800-29265800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr18:29262800-29265800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr18:29262800-29265800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr18:29263000-29264600	Flanking Active TSS	Dnd41	blood
19	chr18:29263000-29265600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:29263000-29265800	Active TSS	Psoas Muscle	Psoas
21	chr18:29263000-29266000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:29263000-29266400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr18:29263200-29264400	Flanking Active TSS	HUVEC	blood vessel
24	chr18:29263200-29265600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:29263200-29265600	Active TSS	Primary T cells from cord blood	blood
26	chr18:29263200-29265600	Active TSS	Duodenum Mucosa	Duodenum
27	chr18:29263200-29265800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:29263200-29265800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr18:29263200-29266200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr18:29263200-29266200	Active TSS	Brain Angular Gyrus	brain
31	chr18:29263200-29266200	Active TSS	Brain Cingulate Gyrus	brain
32	chr18:29263200-29266400	Active TSS	Brain Anterior Caudate	brain
33	chr18:29263200-29266400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr18:29263400-29264200	Active TSS	Brain Germinal Matrix	brain
35	chr18:29263400-29266200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr18:29263400-29266200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr18:29263600-29264200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr18:29263600-29264200	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr18:29263600-29265600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr18:29263600-29265600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr18:29263600-29265800	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr18:29263600-29265800	Active TSS	Right Atrium	heart
43	chr18:29263600-29266000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr18:29263600-29266200	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr18:29263600-29266200	Active TSS	Colon Smooth Muscle	Colon
46	chr18:29263600-29266600	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr18:29263800-29264200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr18:29263800-29264200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr18:29263800-29264200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr18:29263800-29264200	Flanking Active TSS	Fetal Brain Male	brain

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