Variant report

Variant	rs7288576
Chromosome Location	chr22:30603574-30603575
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	SIN3AK20	chr22:30602720-30603577	MCF-7	breast:	n/a	n/a
2	POLR2A	chr22:30603518-30603575	MCF-7	breast:	n/a	n/a
3	GATA3	chr22:30602578-30603651	A549	lung:	n/a	n/a
4	GATA3	chr22:30602723-30603679	MCF-7	breast:	n/a	n/a
5	EP300	chr22:30602637-30603624	A549	lung:	n/a	chr22:30603182-30603189 chr22:30603368-30603382 chr22:30603364-30603378
6	MAX	chr22:30600618-30603846	A549	lung:	n/a	chr22:30601989-30601998
7	TEAD4	chr22:30602676-30603662	SK-N-SH	brain:	n/a	n/a
8	RCOR1	chr22:30602402-30603907	IMR90	lung:	n/a	n/a
9	FOSL2	chr22:30602601-30603794	A549	lung:	n/a	n/a
10	EP300	chr22:30602630-30603714	A549	lung:	n/a	chr22:30603182-30603189 chr22:30603368-30603382 chr22:30603364-30603378
11	POLR2A	chr22:30599869-30607773	IMR90	lung:	n/a	n/a
12	TCF12	chr22:30602577-30603621	A549	lung:	n/a	chr22:30603299-30603307

Variant related genes	Relation type
ENSG00000225676	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1160671	0.83[ASN][1000 genomes]
rs13054837	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13056332	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13057878	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2106430	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2106722	0.81[ASN][1000 genomes]
rs2214047	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412977	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412979	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34391152	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34420020	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34474867	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34545612	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35539897	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4823080	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823081	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4823082	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753027	0.83[ASN][1000 genomes]
rs5753028	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753029	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753030	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5753046	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763825	0.83[ASN][1000 genomes]
rs5763852	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763854	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763861	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5763872	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006393	0.88[ASN][1000 genomes]
rs6006399	0.93[ASN][1000 genomes]
rs975704	0.89[EUR][1000 genomes];0.83[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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7288576	LGALS8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30592800-30604800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr22:30597600-30609800	Enhancers	Stomach Mucosa	stomach
3	chr22:30597600-30610000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr22:30598600-30607000	Enhancers	Placenta	Placenta
5	chr22:30599000-30605200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr22:30599800-30605600	Enhancers	NHLF	lung
7	chr22:30600000-30603600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr22:30600000-30604200	Weak transcription	Fetal Kidney	kidney
9	chr22:30600000-30605000	Weak transcription	Pancreas	Pancrea
10	chr22:30600200-30607800	Enhancers	NH-A	brain
11	chr22:30600400-30606000	Enhancers	Ovary	ovary
12	chr22:30600400-30607000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr22:30600400-30607000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:30600400-30607200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:30600400-30610000	Enhancers	HMEC	breast
16	chr22:30600600-30603800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr22:30600600-30605000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr22:30600800-30606200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr22:30601000-30610000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr22:30601200-30603600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr22:30601400-30605600	Enhancers	HUVEC	blood vessel
22	chr22:30601400-30606600	Enhancers	HepG2	liver
23	chr22:30601600-30604200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr22:30601600-30605600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:30601600-30605800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:30601600-30606600	Enhancers	Hela-S3	cervix
27	chr22:30601800-30603800	Enhancers	NHEK	skin
28	chr22:30601800-30604200	Weak transcription	Colonic Mucosa	Colon
29	chr22:30601800-30604400	Weak transcription	Fetal Thymus	thymus
30	chr22:30601800-30604600	Enhancers	NHDF-Ad	bronchial
31	chr22:30601800-30605400	Weak transcription	Esophagus	oesophagus
32	chr22:30601800-30609800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr22:30601800-30610400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr22:30602000-30603600	Enhancers	Brain Hippocampus Middle	brain
35	chr22:30602000-30603800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr22:30602000-30604000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr22:30602000-30606200	Enhancers	HSMM	muscle
38	chr22:30602000-30607600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr22:30602000-30608400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr22:30602200-30604200	Weak transcription	K562	blood
41	chr22:30602200-30604400	Weak transcription	Colon Smooth Muscle	Colon
42	chr22:30602200-30604600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr22:30602200-30604600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr22:30602200-30606200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr22:30602400-30605800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr22:30602800-30603800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:30602800-30603800	Enhancers	Placenta Amnion	Placenta Amnion
48	chr22:30602800-30604400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr22:30603000-30603600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:30603000-30603600	Enhancers	Brain Substantia Nigra	brain

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