Variant report

Variant	rs1332328
Chromosome Location	chr10:91011458-91011459
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	chr10:91011150-91011965	HEK293	kidney:	n/a	n/a
2	MAX	chr10:91010972-91012069	NB4	blood:	n/a	chr10:91011966-91011975
3	POLR2A	chr10:91011326-91011880	GM10847	blood:	n/a	n/a
4	POU2F2	chr10:91011399-91011603	GM12878	blood:	n/a	n/a
5	TAF1	chr10:91011457-91011620	GM12892	blood:	n/a	n/a
6	REST	chr10:91010938-91011915	U87	brain:	n/a	chr10:91011496-91011505 chr10:91011240-91011249 chr10:91011548-91011558 chr10:91011229-91011249 chr10:91011460-91011473
7	POLR2A	chr10:91011281-91011921	Hela-S3	cervix:	n/a	n/a
8	ELF1	chr10:91011345-91012041	GM12878	blood:	n/a	chr10:91011652-91011663 chr10:91012022-91012033
9	EGR1	chr10:91011408-91012022	ECC-1	luminal epithelium:	n/a	chr10:91011806-91011817 chr10:91011806-91011816 chr10:91011855-91011868 chr10:91011724-91011733
10	PML	chr10:91011251-91011864	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:91011335-91011646	HepG2	liver:	n/a	n/a
12	RAD21	chr10:91011379-91011827	H1-hESC	embryonic stem cell:	n/a	chr10:91011454-91011468
13	EBF1	chr10:91011443-91011955	GM12878	blood:	n/a	n/a
14	MAX	chr10:91010965-91012068	H1-hESC	embryonic stem cell:	n/a	chr10:91011966-91011975
15	POLR2A	chr10:91011405-91011561	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr10:91011207-91011863	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr10:91011290-91011686	A549	lung:	n/a	n/a
18	GABPA	chr10:91010915-91011929	MCF-7	breast:	n/a	chr10:91011811-91011822
19	MAX	chr10:91011364-91012095	SK-N-SH	brain:	n/a	chr10:91011966-91011975
20	MXI1	chr10:91010891-91012146	GM12878	blood:	n/a	n/a
21	CTCF	chr10:91011420-91011570	GM12873	blood:	n/a	n/a
22	MXI1	chr10:91010333-91012194	IMR90	lung:	n/a	n/a
23	MYC	chr10:91010959-91012066	NB4	blood:	n/a	chr10:91011966-91011975
24	ZEB1	chr10:91011221-91011668	GM12878	blood:	n/a	chr10:91011457-91011466 chr10:91011489-91011496
25	MAZ	chr10:91011090-91011942	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr10:91011321-91012028	H1-neurons	neurons:	n/a	n/a
27	SREBP1	chr10:91011321-91011952	HepG2	liver:	n/a	n/a
28	POLR2A	chr10:91010705-91011930	HepG2	liver:	n/a	n/a
29	ZBTB7A	chr10:91011426-91011614	HepG2	liver:	n/a	n/a
30	POLR2A	chr10:91010924-91012095	GM12878	blood:	n/a	n/a
31	POLR2A	chr10:91011330-91012025	MCF10A-Er-Src	breast:	n/a	n/a
32	TBL1XR1	chr10:91011428-91011913	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:91011341-91011651	A549	lung:	n/a	n/a
34	REST	chr10:91011035-91011554	Hela-S3	cervix:	n/a	chr10:91011496-91011505 chr10:91011240-91011249 chr10:91011229-91011249 chr10:91011460-91011473
35	REST	chr10:91011066-91011642	PANC-1	pancreas:	n/a	chr10:91011496-91011505 chr10:91011240-91011249 chr10:91011548-91011558 chr10:91011229-91011249 chr10:91011460-91011473
36	CHD2	chr10:91011333-91011988	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr10:91011337-91011836	HUVEC	blood vessel:	n/a	n/a
38	REST	chr10:91010973-91011634	A549	lung:	n/a	chr10:91011496-91011505 chr10:91011240-91011249 chr10:91011548-91011558 chr10:91011229-91011249 chr10:91011460-91011473
39	MAX	chr10:91010931-91012129	HepG2	liver:	n/a	chr10:91011966-91011975
40	TCF7L2	chr10:91010818-91011686	PANC-1	pancreas:	n/a	n/a
41	TAF1	chr10:91011157-91012039	ECC-1	luminal epithelium:	n/a	n/a
42	ELF1	chr10:91011286-91011985	MCF-7	breast:	n/a	chr10:91011652-91011663
43	HEY1	chr10:91011354-91011674	HepG2	liver:	n/a	chr10:91011467-91011482 chr10:91011470-91011485
44	MAX	chr10:91010985-91012046	GM12878	blood:	n/a	chr10:91011966-91011975
45	POLR2A	chr10:91011357-91011756	HUVEC	blood vessel:	n/a	n/a
46	TCF3	chr10:91011296-91011658	GM12878	blood:	n/a	n/a
47	SP1	chr10:91011215-91012037	A549	lung:	n/a	chr10:91011671-91011682 chr10:91011630-91011651 chr10:91011854-91011863 chr10:91011852-91011864 chr10:91011853-91011862 chr10:91011852-91011864
48	POLR2A	chr10:91011137-91011883	MCF-7	breast:	n/a	n/a
49	SP1	chr10:91011278-91012090	A549	lung:	n/a	chr10:91011671-91011682 chr10:91011630-91011651 chr10:91011854-91011863 chr10:91011852-91011864 chr10:91011853-91011862 chr10:91011852-91011864
50	ELF1	chr10:91011366-91011944	MCF-7	breast:	n/a	chr10:91011652-91011663

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: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1051338	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1332327	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1332329	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1412444	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1412445	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2243547	0.83[EUR][1000 genomes]
rs2246828	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2246833	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246941	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2246942	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250644	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250645	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1332328	LIPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91009400-91012000	Active TSS	Fetal Intestine Large	intestine
2	chr10:91009800-91012000	Active TSS	GM12878-XiMat	blood
3	chr10:91010200-91011600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:91010200-91011800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr10:91010200-91012000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:91010200-91012000	Active TSS	Right Atrium	heart
7	chr10:91010200-91012400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr10:91010400-91011600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr10:91010400-91011600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:91010400-91011800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr10:91010400-91012000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:91010400-91012000	Active TSS	NHDF-Ad	bronchial
13	chr10:91010600-91011600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr10:91010600-91012000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:91010600-91012000	Active TSS	Brain Anterior Caudate	brain
16	chr10:91010600-91012000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:91010600-91012000	Active TSS	Colonic Mucosa	Colon
18	chr10:91010800-91011600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:91010800-91011600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr10:91010800-91011600	Active TSS	Small Intestine	intestine
21	chr10:91010800-91011600	Bivalent/Poised TSS	HepG2	liver
22	chr10:91010800-91011800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr10:91010800-91011800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:91010800-91011800	Active TSS	Aorta	Aorta
25	chr10:91010800-91011800	Active TSS	Brain Cingulate Gyrus	brain
26	chr10:91010800-91011800	Active TSS	Colon Smooth Muscle	Colon
27	chr10:91010800-91011800	Active TSS	Fetal Intestine Small	intestine
28	chr10:91010800-91011800	Active TSS	Gastric	stomach
29	chr10:91010800-91011800	Active TSS	Lung	lung
30	chr10:91010800-91012000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:91010800-91012000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:91010800-91012000	Active TSS	Brain Germinal Matrix	brain
33	chr10:91010800-91012000	Active TSS	Fetal Kidney	kidney
34	chr10:91010800-91012000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr10:91010800-91012000	Active TSS	Ovary	ovary
36	chr10:91010800-91012000	Active TSS	Psoas Muscle	Psoas
37	chr10:91010800-91012000	Active TSS	Right Ventricle	heart
38	chr10:91011000-91011800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:91011000-91011800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr10:91011000-91011800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:91011000-91011800	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr10:91011000-91012000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:91011000-91012000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:91011000-91012000	Active TSS	Rectal Smooth Muscle	rectum
45	chr10:91011000-91012000	Active TSS	A549	lung
46	chr10:91011000-91012000	Active TSS	NHEK	skin
47	chr10:91011000-91012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr10:91011000-91012400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:91011200-91011600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr10:91011200-91011600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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