Variant report

Variant	rs595649
Chromosome Location	chr18:8341610-8341611
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	ATF3	chr18:8341465-8342254	A549	lung:	n/a	n/a
2	EP300	chr18:8341309-8342654	A549	lung:	n/a	chr18:8342167-8342180 chr18:8342057-8342071
3	MAX	chr18:8341527-8342227	A549	lung:	n/a	n/a
4	NFIC	chr18:8341491-8342028	HepG2	liver:	n/a	n/a
5	RXRA	chr18:8341391-8342199	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341843-8341859
6	HNF4G	chr18:8341524-8341996	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
7	RAD21	chr18:8341476-8342156	IMR90	lung:	n/a	chr18:8341605-8341612
8	FOXA2	chr18:8341266-8342501	A549	lung:	n/a	chr18:8341775-8341787
9	HNF4A	chr18:8341454-8342019	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
10	TEAD4	chr18:8341517-8342298	A549	lung:	n/a	n/a
11	PBX3	chr18:8341419-8342248	A549	lung:	n/a	n/a
12	ZBTB33	chr18:8341456-8342204	A549	lung:	n/a	n/a
13	USF1	chr18:8341495-8342768	A549	lung:	n/a	n/a
14	MAX	chr18:8341311-8342447	A549	lung:	n/a	n/a
15	ZBTB7A	chr18:8341501-8341833	HepG2	liver:	n/a	n/a
16	NR3C1	chr18:8341411-8342297	A549	lung:	n/a	chr18:8342103-8342116
17	HDAC2	chr18:8341490-8342208	HepG2	liver:	n/a	n/a
18	MXI1	chr18:8341480-8342319	HepG2	liver:	n/a	n/a
19	HNF4A	chr18:8341602-8341963	HepG2	liver:	n/a	chr18:8341695-8341711 chr18:8341661-8341669
20	JUN	chr18:8341562-8342023	HepG2	liver:	n/a	chr18:8341681-8341690 chr18:8341680-8341689
21	TEAD4	chr18:8341365-8342310	A549	lung:	n/a	n/a
22	FOSL2	chr18:8341370-8341988	HepG2	liver:	n/a	chr18:8341459-8341470 chr18:8341681-8341690 chr18:8341680-8341689
23	JUND	chr18:8341403-8342332	A549	lung:	n/a	chr18:8341459-8341470 chr18:8341681-8341690 chr18:8341680-8341689
24	MAX	chr18:8341217-8342467	A549	lung:	n/a	n/a
25	MYBL2	chr18:8341474-8342110	HepG2	liver:	n/a	n/a
26	PBX3	chr18:8341525-8342212	A549	lung:	n/a	n/a
27	RAD21	chr18:8341541-8342082	A549	lung:	n/a	chr18:8341605-8341612
28	NFIC	chr18:8341407-8342090	HepG2	liver:	n/a	n/a
29	YY1	chr18:8341422-8342202	A549	lung:	n/a	chr18:8341930-8341938 chr18:8341919-8341941 chr18:8341931-8341941
30	SIN3AK20	chr18:8341499-8341961	A549	lung:	n/a	n/a
31	MBD4	chr18:8341530-8342038	HepG2	liver:	n/a	n/a
32	EP300	chr18:8341479-8342151	HepG2	liver:	n/a	chr18:8342057-8342071
33	CEBPB	chr18:8341487-8342380	A549	lung:	n/a	n/a
34	NR3C1	chr18:8341374-8342287	A549	lung:	n/a	chr18:8342103-8342116
35	CREB1	chr18:8341418-8342282	A549	lung:	n/a	n/a
36	MAFK	chr18:8341570-8342341	HepG2	liver:	n/a	chr18:8342013-8342027 chr18:8342014-8342025
37	TCF12	chr18:8341489-8342222	A549	lung:	n/a	n/a
38	MAX	chr18:8341530-8341967	HepG2	liver:	n/a	n/a
39	RCOR1	chr18:8341601-8342203	HepG2	liver:	n/a	n/a
40	CEBPB	chr18:8341515-8342321	HepG2	liver:	n/a	n/a
41	JUND	chr18:8341482-8342066	HepG2	liver:	n/a	chr18:8341681-8341690 chr18:8341680-8341689
42	BRCA1	chr18:8341476-8341715	HepG2	liver:	n/a	n/a
43	MYBL2	chr18:8341479-8342139	HepG2	liver:	n/a	n/a
44	EP300	chr18:8341452-8342189	HepG2	liver:	n/a	chr18:8342167-8342180 chr18:8342057-8342071
45	CREB1	chr18:8341354-8342063	A549	lung:	n/a	n/a
46	CEBPB	chr18:8341556-8342240	HepG2	liver:	n/a	n/a
47	FOXA2	chr18:8341286-8342439	A549	lung:	n/a	chr18:8341775-8341787
48	NR3C1	chr18:8341209-8342673	A549	lung:	n/a	chr18:8342103-8342116
49	ARID3A	chr18:8341386-8342209	HepG2	liver:	n/a	n/a
50	FOXA1	chr18:8341420-8342009	HepG2	liver:	n/a	chr18:8341775-8341787

Variant related genes	Relation type
ENSG00000268046	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11873699	0.88[YRI][hapmap]
rs11876786	1.00[YRI][hapmap]
rs11877672	0.88[YRI][hapmap]
rs12456630	0.81[MKK][hapmap];1.00[YRI][hapmap]
rs17490458	0.84[JPT][hapmap];0.88[YRI][hapmap]
rs17490807	0.88[YRI][hapmap]
rs17490828	0.88[YRI][hapmap]
rs2279074	1.00[YRI][hapmap]
rs2279075	1.00[YRI][hapmap]
rs4511600	0.89[CEU][hapmap]
rs594691	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60239768	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7244164	0.88[YRI][hapmap]
rs8087223	0.88[YRI][hapmap]

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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458018	chr18:8110805-8645907	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv576426	chr18:8110805-8645907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057288	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv543639	chr18:8218725-8351340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3351324	chr18:8250514-8405140	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1058445	chr18:8270681-8421249	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs595649	APCDD1	cis	cerebellum	SCAN
rs595649	NAPG	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8320800-8357200	Weak transcription	Thymus	Thymus
2	chr18:8328000-8342600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr18:8329600-8358200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:8329800-8365200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:8334400-8341800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:8339400-8342000	Enhancers	Right Atrium	heart
7	chr18:8339400-8342200	Enhancers	Left Ventricle	heart
8	chr18:8339400-8342200	Enhancers	Right Ventricle	heart
9	chr18:8339400-8342600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr18:8339400-8344200	Enhancers	Fetal Heart	heart
11	chr18:8339600-8342200	Enhancers	Pancreas	Pancrea
12	chr18:8339600-8344000	Enhancers	Fetal Lung	lung
13	chr18:8340200-8344200	Weak transcription	Brain Anterior Caudate	brain
14	chr18:8340200-8365600	Weak transcription	Psoas Muscle	Psoas
15	chr18:8340400-8342200	Enhancers	Aorta	Aorta
16	chr18:8340800-8341800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr18:8340800-8343000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:8340800-8344200	Enhancers	Stomach Mucosa	stomach
19	chr18:8341000-8342000	Enhancers	HSMMtube	muscle
20	chr18:8341000-8342200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr18:8341000-8343000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr18:8341000-8343000	Enhancers	Liver	Liver
23	chr18:8341200-8342400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:8341200-8342600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:8341200-8342600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:8341200-8342600	Enhancers	NH-A	brain
27	chr18:8341200-8342600	Enhancers	Osteobl	bone
28	chr18:8341200-8343800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr18:8341400-8341800	Enhancers	Small Intestine	intestine
30	chr18:8341400-8342000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr18:8341400-8342000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr18:8341400-8342000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr18:8341400-8342000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr18:8341400-8342000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr18:8341400-8342000	Enhancers	Fetal Muscle Trunk	muscle
36	chr18:8341400-8342000	Enhancers	Ovary	ovary
37	chr18:8341400-8342000	Enhancers	Stomach Smooth Muscle	stomach
38	chr18:8341400-8342200	Enhancers	Fetal Intestine Small	intestine
39	chr18:8341400-8342200	Enhancers	Fetal Stomach	stomach
40	chr18:8341400-8342200	Enhancers	Gastric	stomach
41	chr18:8341400-8342200	Enhancers	Lung	lung
42	chr18:8341400-8342200	Flanking Active TSS	HepG2	liver
43	chr18:8341400-8342400	Enhancers	NHDF-Ad	bronchial
44	chr18:8341400-8342400	Enhancers	NHLF	lung
45	chr18:8341400-8342600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr18:8341400-8342800	Enhancers	Fetal Kidney	kidney
47	chr18:8341400-8343600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr18:8341600-8342000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr18:8341600-8342000	Enhancers	Fetal Intestine Large	intestine
50	chr18:8341600-8342200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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