Variant report

Variant	rs2243547
Chromosome Location	chr10:91010479-91010480
allele	G/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	MXI1	chr10:91010333-91012194	IMR90	lung:	n/a	n/a
2	GATA3	chr10:91010472-91011133	MCF-7	breast:	n/a	chr10:91010773-91010783 chr10:91010775-91010782 chr10:91010774-91010782 chr10:91010773-91010782 chr10:91010770-91010786 chr10:91010775-91010782 chr10:91010775-91010782 chr10:91010768-91010789
3	POLR2A	chr10:91010320-91011839	HepG2	liver:	n/a	n/a
4	GATA3	chr10:91010407-91011248	SK-N-SH	brain:	n/a	chr10:91010773-91010783 chr10:91010775-91010782 chr10:91010774-91010782 chr10:91010773-91010782 chr10:91010770-91010786 chr10:91010775-91010782 chr10:91010775-91010782 chr10:91010768-91010789
5	GATA2	chr10:91010373-91012017	SH-SY5Y	brain:	n/a	chr10:91010773-91010783 chr10:91010775-91010782 chr10:91011555-91011564 chr10:91011953-91011962 chr10:91010773-91010782 chr10:91010770-91010786 chr10:91010775-91010782 chr10:91010775-91010782 chr10:91010768-91010789
6	TBP	chr10:91009996-91010565	HepG2	liver:	n/a	n/a
7	MXI1	chr10:91010270-91012216	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr10:91010427-91010988	SH-SY5Y	brain:	n/a	chr10:91010773-91010783 chr10:91010775-91010782 chr10:91010774-91010782 chr10:91010773-91010782 chr10:91010770-91010786 chr10:91010775-91010782 chr10:91010775-91010782 chr10:91010768-91010789

No.	Distal block	Cell Line	Cell type
1	chr10:91009631..91012227-chr10:91174311..91176643,2	MCF-7	breast:
2	chr10:90610616..90613278-chr10:91010263..91012632,2	MCF-7	breast:
3	chr10:91004556..91008070-chr10:91009861..91011850,3	MCF-7	breast:

Variant related genes	Relation type
LIPA	TF binding region
ENSG00000152766	Chromatin interaction
ENSG00000152778	Chromatin interaction
ENSG00000107798	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1051338	0.92[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1332327	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332328	0.83[EUR][1000 genomes]
rs1332329	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1412444	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1412445	0.84[EUR][1000 genomes]
rs2246828	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2246833	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246941	0.84[EUR][1000 genomes]
rs2246942	0.86[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250644	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250645	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758235	chr10:90835064-91017486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759775	chr10:90835064-91017486	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv895882	chr10:91002927-91021645	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv520796	chr10:91007470-91010479	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2243547	LIPA	cis	cerebellum	SCAN
rs2243547	LIPA	Cis_1M	lymphoblastoid	RTeQTL
rs2243547	ANKRD1	cis	parietal	SCAN
rs2243547	LIPA	cis	Whole Blood	GTEx
rs2243547	LIPK	cis	parietal	SCAN
rs2243547	LIPA	cis	lung	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:90985200-91010600	Weak transcription	Thymus	Thymus
4	chr10:90987400-91010800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:90987600-91010800	Weak transcription	Pancreas	Pancrea
6	chr10:90987800-91010600	Weak transcription	HSMM	muscle
7	chr10:90988000-91010600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:90994800-91010800	Weak transcription	Esophagus	oesophagus
9	chr10:90999800-91010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:90999800-91010600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr10:90999800-91010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:90999800-91010800	Weak transcription	Ovary	ovary
13	chr10:91000000-91010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr10:91000200-91010600	Weak transcription	Brain Germinal Matrix	brain
15	chr10:91000200-91010600	Weak transcription	Fetal Brain Female	brain
16	chr10:91000600-91010800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:91001000-91010600	Weak transcription	Fetal Stomach	stomach
18	chr10:91001000-91010600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr10:91001200-91010600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:91001200-91010800	Weak transcription	Lung	lung
21	chr10:91002200-91010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:91002400-91010800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:91002400-91010800	Weak transcription	Left Ventricle	heart
24	chr10:91002800-91010600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:91003200-91010600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:91003200-91010600	Weak transcription	Placenta	Placenta
27	chr10:91003200-91010600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:91003600-91010800	Weak transcription	Aorta	Aorta
29	chr10:91003600-91010800	Weak transcription	Spleen	Spleen
30	chr10:91004200-91010600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:91006000-91010800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr10:91006200-91010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:91006200-91010600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:91008400-91010800	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr10:91009000-91010600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr10:91009400-91012000	Active TSS	Fetal Intestine Large	intestine
37	chr10:91009800-91010600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:91009800-91010600	Enhancers	Primary B cells from peripheral blood	blood
39	chr10:91009800-91012000	Active TSS	GM12878-XiMat	blood
40	chr10:91010000-91010800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr10:91010000-91010800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr10:91010000-91010800	Active TSS	Brain Angular Gyrus	brain
43	chr10:91010000-91010800	Active TSS	HepG2	liver
44	chr10:91010200-91010600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr10:91010200-91010600	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr10:91010200-91010600	Active TSS	Duodenum Mucosa	Duodenum
47	chr10:91010200-91010600	Enhancers	A549	lung
48	chr10:91010200-91010600	Enhancers	Hela-S3	cervix
49	chr10:91010200-91010800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr10:91010200-91010800	Flanking Active TSS	Fetal Intestine Small	intestine

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