Variant report

Variant	rs1332327
Chromosome Location	chr10:91011681-91011682
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	YY1	chr10:91011616-91011952	GM12891	blood:	n/a	chr10:91011686-91011697
5	REST	chr10:91010938-91011915	U87	brain:	n/a	chr10:91011496-91011505 chr10:91011240-91011249 chr10:91011548-91011558 chr10:91011229-91011249 chr10:91011460-91011473
6	POLR2A	chr10:91011281-91011921	Hela-S3	cervix:	n/a	n/a
7	ELF1	chr10:91011345-91012041	GM12878	blood:	n/a	chr10:91011652-91011663 chr10:91012022-91012033
8	POLR2A	chr10:91011656-91011854	GM12891	blood:	n/a	n/a
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	E2F6	chr10:91011623-91011992	A549	lung:	n/a	chr10:91011631-91011640
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	PAX5	chr10:91011626-91011874	GM12878	blood:	n/a	n/a
15	MAX	chr10:91010965-91012068	H1-hESC	embryonic stem cell:	n/a	chr10:91011966-91011975
16	POLR2A	chr10:91011619-91011846	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr10:91011207-91011863	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr10:91011290-91011686	A549	lung:	n/a	n/a
19	GABPA	chr10:91010915-91011929	MCF-7	breast:	n/a	chr10:91011811-91011822
20	MAX	chr10:91011364-91012095	SK-N-SH	brain:	n/a	chr10:91011966-91011975
21	TBP	chr10:91011495-91011959	GM12878	blood:	n/a	n/a
22	MXI1	chr10:91010891-91012146	GM12878	blood:	n/a	n/a
23	MXI1	chr10:91010333-91012194	IMR90	lung:	n/a	n/a
24	E2F6	chr10:91011495-91012081	A549	lung:	n/a	chr10:91011631-91011640
25	MYC	chr10:91010959-91012066	NB4	blood:	n/a	chr10:91011966-91011975
26	NFYB	chr10:91011570-91011827	K562	blood:	n/a	chr10:91011629-91011642 chr10:91011629-91011643 chr10:91011629-91011644 chr10:91011629-91011644 chr10:91011631-91011641 chr10:91011628-91011640
27	MAZ	chr10:91011090-91011942	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr10:91011321-91012028	H1-neurons	neurons:	n/a	n/a
29	SREBP1	chr10:91011321-91011952	HepG2	liver:	n/a	n/a
30	POLR2A	chr10:91010705-91011930	HepG2	liver:	n/a	n/a
31	POLR2A	chr10:91010924-91012095	GM12878	blood:	n/a	n/a
32	POLR2A	chr10:91011330-91012025	MCF10A-Er-Src	breast:	n/a	n/a
33	TBL1XR1	chr10:91011428-91011913	GM12878	blood:	n/a	n/a
34	CHD2	chr10:91011333-91011988	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr10:91011337-91011836	HUVEC	blood vessel:	n/a	n/a
36	MAX	chr10:91010931-91012129	HepG2	liver:	n/a	chr10:91011966-91011975
37	TCF7L2	chr10:91010818-91011686	PANC-1	pancreas:	n/a	n/a
38	TAF1	chr10:91011157-91012039	ECC-1	luminal epithelium:	n/a	n/a
39	ELF1	chr10:91011286-91011985	MCF-7	breast:	n/a	chr10:91011652-91011663
40	CTCF	chr10:91011600-91011750	SAEC	small airway:	n/a	n/a
41	NRF1	chr10:91011496-91012032	GM12878	blood:	n/a	chr10:91011811-91011822
42	MAX	chr10:91010985-91012046	GM12878	blood:	n/a	chr10:91011966-91011975
43	POLR2A	chr10:91011357-91011756	HUVEC	blood vessel:	n/a	n/a
44	ARID3A	chr10:91011635-91012246	HepG2	liver:	n/a	n/a
45	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
46	POLR2A	chr10:91011137-91011883	MCF-7	breast:	n/a	n/a
47	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
48	ELF1	chr10:91011366-91011944	MCF-7	breast:	n/a	chr10:91011652-91011663
49	POLR2A	chr10:91011245-91012080	PANC-1	pancreas:	n/a	n/a
50	SIN3A	chr10:91010969-91011953	H1-hESC	embryonic stem cell:	n/a	chr10:91011493-91011502

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:91011667-91011717	A549	lung:	n/a
2	chr10:91011667-91011717	SK-N-MC	brain:	n/a
3	chr10:91011676-91011726	AG10803	skin:	n/a
4	chr10:91011667-91011717	Jurkat	blood:	n/a
5	chr10:91011667-91011717	ProgFib	skin:	n/a
6	chr10:91011676-91011726	SK-N-SH	brain:	n/a
7	chr10:91011667-91011717	GM19239	blood:	n/a
8	chr10:91011676-91011726	MCF-7	breast:	n/a
9	chr10:91011676-91011726	AG09319	gingival:	n/a
10	chr10:91011676-91011726	NHDF-neo	bronchial:	n/a
11	chr10:91011676-91011726	H1-hESC	embryonic stem cell:	embryo
12	chr10:91011676-91011726	GM19239	blood:	n/a
13	chr10:91011667-91011717	SAEC	small airway:	n/a
14	chr10:91011667-91011717	AG09309	skin:	n/a
15	chr10:91011667-91011717	PANC-1	pancreas:	n/a
16	chr10:91011667-91011717	BE2_C	brain:	n/a
17	chr10:91011676-91011726	SAEC	small airway:	n/a
18	chr10:91011676-91011726	GM06990	blood:	n/a
19	chr10:91011667-91011717	NT2-D1	testis:	n/a
20	chr10:91011676-91011726	NT2-D1	testis:	n/a
21	chr10:91011667-91011717	HNPCEpiC	eye:	n/a
22	chr10:91011676-91011726	AoSMC	blood vessel:	n/a
23	chr10:91011676-91011726	HUVEC	blood vessel:	n/a
24	chr10:91011676-91011726	Jurkat	blood:	n/a
25	chr10:91011676-91011726	HEEpiC	esophagus:	n/a
26	chr10:91011676-91011726	HCT-116	colon:	n/a
27	chr10:91011667-91011717	NH-A	brain:	n/a
28	chr10:91011676-91011726	ovcar-3	ovarian:	n/a
29	chr10:91011676-91011726	HRE	kidney:	n/a
30	chr10:91011667-91011717	GM12892	blood:	n/a
31	chr10:91011676-91011726	HL-60	blood:	n/a
32	chr10:91011667-91011717	AG10803	skin:	n/a
33	chr10:91011667-91011717	HepG2	liver:	n/a
34	chr10:91011676-91011726	PANC-1	pancreas:	n/a
35	chr10:91011676-91011726	SK-N-SH_RA	brain:	n/a
36	chr10:91011667-91011717	GM12878	blood:	n/a
37	chr10:91011667-91011717	HIPEpiC	eye:	n/a
38	chr10:91011676-91011726	Hela-S3	cervix:	n/a
39	chr10:91011667-91011717	AG04450	lung:	fetal
40	chr10:91011676-91011726	K562	blood:	n/a
41	chr10:91011676-91011726	ECC-1	luminal epithelium:	n/a
42	chr10:91011667-91011717	AG04449	skin:	fetal
43	chr10:91011676-91011726	HRCEpiC	kidney:	n/a
44	chr10:91011667-91011717	H1-hESC	embryonic stem cell:	embryo
45	chr10:91011667-91011717	Hela-S3	cervix:	n/a
46	chr10:91011676-91011726	NB4	blood:	n/a
47	chr10:91011667-91011717	NHBE	bronchial:	n/a
48	chr10:91011667-91011717	HCF	heart:	n/a
49	chr10:91011667-91011717	ovcar-3	ovarian:	n/a
50	chr10:91011676-91011726	HCF	heart:	n/a

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
LIPA	CpG island
ENSG00000107798	Chromatin interaction
ENSG00000152778	Chromatin interaction
ENSG00000152766	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1051338	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1332328	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1332329	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs1412444	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2243547	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]
rs2246828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246833	0.95[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246941	0.81[CHB][hapmap]
rs2246942	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2250644	0.82[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250645	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1332327	LIPA	Cis_1M	lymphoblastoid	RTeQTL
rs1332327	LIPA	cis	lung	GTEx

Chromatin state (count:119 , 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	chr10:91010200-91011800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr10:91010200-91012000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:91010200-91012000	Active TSS	Right Atrium	heart
6	chr10:91010200-91012400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr10:91010400-91011800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr10:91010400-91012000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:91010400-91012000	Active TSS	NHDF-Ad	bronchial
10	chr10:91010600-91012000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:91010600-91012000	Active TSS	Brain Anterior Caudate	brain
12	chr10:91010600-91012000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:91010600-91012000	Active TSS	Colonic Mucosa	Colon
14	chr10:91010800-91011800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:91010800-91011800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:91010800-91011800	Active TSS	Aorta	Aorta
17	chr10:91010800-91011800	Active TSS	Brain Cingulate Gyrus	brain
18	chr10:91010800-91011800	Active TSS	Colon Smooth Muscle	Colon
19	chr10:91010800-91011800	Active TSS	Fetal Intestine Small	intestine
20	chr10:91010800-91011800	Active TSS	Gastric	stomach
21	chr10:91010800-91011800	Active TSS	Lung	lung
22	chr10:91010800-91012000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:91010800-91012000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr10:91010800-91012000	Active TSS	Brain Germinal Matrix	brain
25	chr10:91010800-91012000	Active TSS	Fetal Kidney	kidney
26	chr10:91010800-91012000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr10:91010800-91012000	Active TSS	Ovary	ovary
28	chr10:91010800-91012000	Active TSS	Psoas Muscle	Psoas
29	chr10:91010800-91012000	Active TSS	Right Ventricle	heart
30	chr10:91011000-91011800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:91011000-91011800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:91011000-91011800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:91011000-91011800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr10:91011000-91012000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:91011000-91012000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr10:91011000-91012000	Active TSS	Rectal Smooth Muscle	rectum
37	chr10:91011000-91012000	Active TSS	A549	lung
38	chr10:91011000-91012000	Active TSS	NHEK	skin
39	chr10:91011000-91012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr10:91011000-91012400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:91011200-91011800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr10:91011200-91011800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:91011200-91011800	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr10:91011200-91011800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr10:91011200-91011800	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr10:91011200-91011800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr10:91011200-91011800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr10:91011200-91011800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:91011200-91011800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:91011200-91011800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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