Variant report

Variant	rs28424062
Chromosome Location	chr18:6963744-6963745
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	ARID3A	chr18:6963678-6964212	HepG2	liver:	n/a	chr18:6963779-6963795 chr18:6963778-6963794
2	EP300	chr18:6963473-6963998	HepG2	liver:	n/a	n/a
3	HNF4A	chr18:6963656-6964024	HepG2	liver:	n/a	chr18:6963733-6963741
4	MYBL2	chr18:6963536-6964088	HepG2	liver:	n/a	n/a
5	JUND	chr18:6963712-6964504	HepG2	liver:	n/a	n/a
6	CEBPB	chr18:6963661-6964505	HepG2	liver:	n/a	n/a
7	HNF4G	chr18:6963564-6963847	HepG2	liver:	n/a	chr18:6963733-6963741
8	NFIC	chr18:6963462-6964037	HepG2	liver:	n/a	n/a
9	FOXA1	chr18:6963633-6964091	HepG2	liver:	n/a	n/a
10	HNF4A	chr18:6962626-6963909	HepG2	liver:	n/a	chr18:6962703-6962711 chr18:6962801-6962815 chr18:6963264-6963276 chr18:6962800-6962815 chr18:6963263-6963278 chr18:6962802-6962814 chr18:6962800-6962815 chr18:6963270-6963278 chr18:6963265-6963277 chr18:6962802-6962815 chr18:6962800-6962815 chr18:6962801-6962815 chr18:6962802-6962814 chr18:6963263-6963276 chr18:6963263-6963276 chr18:6963733-6963741 chr18:6963264-6963276 chr18:6962800-6962815 chr18:6962802-6962814 chr18:6962801-6962813 chr18:6963264-6963276 chr18:6963263-6963277 chr18:6963263-6963278 chr18:6963269-6963277 chr18:6963263-6963278 chr18:6962801-6962814 chr18:6962802-6962814 chr18:6963262-6963277 chr18:6962800-6962815 chr18:6963264-6963277 chr18:6962799-6962817

Variant related genes	Relation type
LAMA1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28597704	1.00[AFR][1000 genomes]
rs7242178	1.00[AFR][1000 genomes]
rs9947188	1.00[AFR][1000 genomes]
rs9951050	1.00[AFR][1000 genomes]
rs9956659	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1064175	chr18:6740267-7384528	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv576397	chr18:6758921-7036683	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1059956	chr18:6786579-7382339	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv543632	chr18:6786579-7382339	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv1060826	chr18:6846443-6983289	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv1059970	chr18:6846443-7281397	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv543633	chr18:6846443-7281397	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv1064956	chr18:6846503-7281337	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv543634	chr18:6846503-7281337	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv833583	chr18:6863008-7011756	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
16	esv3584943	chr18:6873354-7434329	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv817574	chr18:6894969-7577149	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
18	nsv868851	chr18:6947043-7470214	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6939000-6978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:6941200-6995000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr18:6945600-6968000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr18:6948600-6977600	Weak transcription	Ovary	ovary
5	chr18:6950200-6977400	Weak transcription	Brain Germinal Matrix	brain
6	chr18:6951000-7007600	Weak transcription	Osteobl	bone
7	chr18:6951400-6964200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:6952000-6975400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr18:6952000-7000200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr18:6952400-6987000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:6954800-6978000	Weak transcription	Brain Anterior Caudate	brain
12	chr18:6957800-6964400	Weak transcription	Pancreas	Pancrea
13	chr18:6957800-6986800	Weak transcription	Right Atrium	heart
14	chr18:6957800-7020800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:6958800-6965600	Weak transcription	Fetal Brain Male	brain
16	chr18:6959200-6965400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr18:6959800-6965400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:6960400-6964800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr18:6960400-6966400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:6960400-6985200	Weak transcription	Brain Hippocampus Middle	brain
21	chr18:6960600-7000400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr18:6960600-7022800	Weak transcription	Fetal Brain Female	brain
23	chr18:6960600-7026400	Weak transcription	Brain Substantia Nigra	brain
24	chr18:6961000-6964400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr18:6961000-6967600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr18:6961000-6986200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:6961000-7007200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:6961200-6965800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:6961400-6963800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr18:6961400-7004000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:6961600-7003800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr18:6961800-6964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:6961800-6992200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr18:6962200-6967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:6962400-6978200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr18:6962600-6964800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr18:6963000-6964600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:6963000-6964800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:6963000-6966400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr18:6963200-6964600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr18:6963200-6964800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr18:6963200-6964800	Strong transcription	Fetal Kidney	kidney
43	chr18:6963400-6964400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:6963400-6964600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr18:6963400-6964600	Strong transcription	Hela-S3	cervix
46	chr18:6963400-6975200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr18:6963600-6964600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr18:6963600-6965000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr18:6963600-6965200	Enhancers	HepG2	liver
50	chr18:6963600-6966400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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