Variant report

Variant	rs2250644
Chromosome Location	chr10:91008879-91008880
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	RUNX3	chr10:91008626-91009146	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:91008724-91008906	GM12878	blood:	n/a	n/a
3	RUNX3	chr10:91008542-91009183	GM12878	blood:	n/a	n/a
4	TBP	chr10:91008714-91008957	GM12878	blood:	n/a	n/a
5	IKZF1	chr10:91008739-91009088	GM12878	blood:	n/a	n/a
6	MAFK	chr10:91008744-91009000	HepG2	liver:	n/a	chr10:91008873-91008884 chr10:91008873-91008884 chr10:91008874-91008885 chr10:91008869-91008885 chr10:91008874-91008885 chr10:91008872-91008886

Variant related genes	Relation type
LIPA	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1051338	0.80[CHB][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1332327	0.82[CEU][hapmap];0.80[CHB][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1332328	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1332329	0.82[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1412444	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1412445	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2243547	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2246828	0.81[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2246833	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2246941	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2246942	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2250645	0.83[EUR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2250644	LIPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90977400-91010400	Weak transcription	Fetal Thymus	thymus
2	chr10:90977400-91010800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr10:90977600-91009400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:90977600-91010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:90977600-91010800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:90985200-91010600	Weak transcription	Thymus	Thymus
7	chr10:90987400-91010800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:90987600-91010800	Weak transcription	Pancreas	Pancrea
9	chr10:90987800-91010600	Weak transcription	HSMM	muscle
10	chr10:90988000-91010600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:90994800-91010800	Weak transcription	Esophagus	oesophagus
12	chr10:90999600-91010400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:90999800-91010000	Weak transcription	Dnd41	blood
14	chr10:90999800-91010400	Weak transcription	Colon Smooth Muscle	Colon
15	chr10:90999800-91010400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:90999800-91010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:90999800-91010600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:90999800-91010800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:90999800-91010800	Weak transcription	Ovary	ovary
20	chr10:91000000-91010400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr10:91000000-91010600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr10:91000200-91010600	Weak transcription	Brain Germinal Matrix	brain
23	chr10:91000200-91010600	Weak transcription	Fetal Brain Female	brain
24	chr10:91000600-91010400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr10:91000600-91010800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr10:91001000-91010600	Weak transcription	Fetal Stomach	stomach
27	chr10:91001000-91010600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:91001200-91009400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr10:91001200-91010600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr10:91001200-91010800	Weak transcription	Lung	lung
31	chr10:91002000-91009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:91002200-91010200	Weak transcription	Hela-S3	cervix
33	chr10:91002200-91010400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:91002200-91010400	Weak transcription	Fetal Lung	lung
35	chr10:91002200-91010600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:91002400-91010200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr10:91002400-91010200	Weak transcription	Fetal Intestine Small	intestine
38	chr10:91002400-91010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:91002400-91010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:91002400-91010800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:91002400-91010800	Weak transcription	Left Ventricle	heart
42	chr10:91002800-91009400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:91002800-91010200	Weak transcription	NHEK	skin
44	chr10:91002800-91010400	Weak transcription	Osteobl	bone
45	chr10:91002800-91010600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:91003000-91009600	Weak transcription	Liver	Liver
47	chr10:91003000-91010400	Weak transcription	Small Intestine	intestine
48	chr10:91003200-91009400	Weak transcription	Brain Anterior Caudate	brain
49	chr10:91003200-91010000	Weak transcription	HMEC	breast
50	chr10:91003200-91010200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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