Variant report

Variant	rs4933497
Chromosome Location	chr10:90968103-90968104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr10:90966529-90968646	HEK293-T-REx	kidney:	n/a	n/a
2	CTCF	chr10:90968000-90968150	GM12871	blood:	n/a	n/a
3	RAD21	chr10:90967547-90968289	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr10:90967452-90968407	H1-hESC	embryonic stem cell:	n/a	chr10:90967985-90967997 chr10:90967914-90967928
5	CTCF	chr10:90968100-90968250	HRE	kidney:	n/a	n/a
6	RAD21	chr10:90967553-90968269	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr10:90967585-90968181	H1-hESC	embryonic stem cell:	n/a	chr10:90967985-90967997 chr10:90967914-90967928
8	JUND	chr10:90967902-90968213	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr10:90967506-90968233	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr10:90966724-90968174	H1-neurons	neurons:	n/a	n/a
11	SIN3A	chr10:90966852-90968132	H1-hESC	embryonic stem cell:	n/a	chr10:90967717-90967726 chr10:90967710-90967723
12	CTBP2	chr10:90967588-90968408	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF2	chr10:90967890-90968348	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr10:90967911-90968202	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr10:90967587-90968424	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:90968091-90968141	Jurkat	blood:	n/a
2	chr10:90968091-90968141	HCM	heart:	n/a
3	chr10:90968091-90968141	RPTEC	kidney:	n/a
4	chr10:90968091-90968141	T-47D	breast:	n/a
5	chr10:90968091-90968141	GM12892	blood:	n/a
6	chr10:90968091-90968141	U87	brain:	n/a
7	chr10:90968091-90968141	SKMC	muscle:	n/a
8	chr10:90968091-90968141	AG09319	gingival:	n/a
9	chr10:90968091-90968141	MCF-7	breast:	n/a
10	chr10:90968091-90968141	GM12891	blood:	n/a
11	chr10:90968091-90968141	HIPEpiC	eye:	n/a
12	chr10:90968091-90968141	GM06990	blood:	n/a
13	chr10:90968091-90968141	HRCEpiC	kidney:	n/a
14	chr10:90968091-90968141	A549	lung:	n/a
15	chr10:90968091-90968141	SK-N-SH_RA	brain:	n/a
16	chr10:90968091-90968141	CMK	blood:	n/a
17	chr10:90968091-90968141	BJ	skin:	n/a
18	chr10:90968091-90968141	HPAEpiC	pulmonary alveolar:	n/a
19	chr10:90968091-90968141	SK-N-MC	brain:	n/a
20	chr10:90968091-90968141	HEK293	kidney:	embryo
21	chr10:90968091-90968141	Hepatocyte	liver:	n/a
22	chr10:90968091-90968141	K562	blood:	n/a
23	chr10:90968091-90968141	PANC-1	pancreas:	n/a
24	chr10:90968091-90968141	AG04449	skin:	fetal
25	chr10:90968091-90968141	BE2_C	brain:	n/a
26	chr10:90968091-90968141	LNCaP	prostate:	n/a
27	chr10:90968091-90968141	NB4	blood:	n/a
28	chr10:90968091-90968141	NH-A	brain:	n/a
29	chr10:90968091-90968141	AG10803	skin:	n/a
30	chr10:90968091-90968141	ProgFib	skin:	n/a
31	chr10:90968091-90968141	PFSK-1	brain:	n/a
32	chr10:90968091-90968141	HMEC	breast:	n/a
33	chr10:90968091-90968141	IMR90	lung:	fetal
34	chr10:90968091-90968141	AG09309	skin:	n/a
35	chr10:90968091-90968141	H1-hESC	embryonic stem cell:	embryo
36	chr10:90968091-90968141	HAEpiC	amniotic membrane:	n/a
37	chr10:90968091-90968141	ovcar-3	ovarian:	n/a
38	chr10:90968091-90968141	MCF10A-Er-Src	breast:	n/a
39	chr10:90968091-90968141	HL-60	blood:	n/a
40	chr10:90968091-90968141	AoSMC	blood vessel:	n/a
41	chr10:90968091-90968141	HepG2	liver:	n/a
42	chr10:90968091-90968141	AG04450	lung:	fetal
43	chr10:90968091-90968141	SAEC	small airway:	n/a
44	chr10:90968091-90968141	NHDF-neo	bronchial:	n/a
45	chr10:90968091-90968141	HUVEC	blood vessel:	n/a
46	chr10:90968091-90968141	HRPEpiC	eye:	n/a
47	chr10:90968091-90968141	NT2-D1	testis:	n/a
48	chr10:90968091-90968141	HEEpiC	esophagus:	n/a
49	chr10:90968091-90968141	Hela-S3	cervix:	n/a
50	chr10:90968091-90968141	GM12878	blood:	n/a

No data

Variant related genes	Relation type
CH25H	TF binding region
CH25H	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11594137	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12780342	0.90[CHD][hapmap]
rs17382301	0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2297475	1.00[JPT][hapmap]
rs34419176	1.00[ASN][1000 genomes]
rs35104206	1.00[ASN][1000 genomes]
rs3802656	0.84[CHD][hapmap]
rs7089138	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908760	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv517170	chr10:90931602-90975207	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv437127	chr10:90940003-90968103	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv467422	chr10:90940687-90975207	Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv467423	chr10:90940687-90975207	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv551858	chr10:90940687-90975207	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1038123	chr10:90954417-90992129	Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1040280	chr10:90962032-90979093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1042428	chr10:90962252-90977164	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4933497	LIPA	cis	cerebellum	SCAN
rs4933497	LIPA	cis	parietal	SCAN
rs4933497	LIPN	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90965600-90968400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr10:90966000-90968400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:90966200-90968200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr10:90966200-90968200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
5	chr10:90966200-90968200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
6	chr10:90966200-90968200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
7	chr10:90966200-90968200	Bivalent/Poised TSS	A549	lung
8	chr10:90966200-90968400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
9	chr10:90966200-90968400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
10	chr10:90966200-90968400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:90966200-90968400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr10:90966200-90968400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
13	chr10:90966200-90968600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr10:90966400-90968200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
15	chr10:90966400-90968200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr10:90966400-90968200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:90966400-90968200	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
18	chr10:90966400-90968200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
19	chr10:90966400-90968200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
20	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
21	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
22	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
23	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
24	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:90966400-90968400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
26	chr10:90966600-90968200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
27	chr10:90966600-90968200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:90966600-90968200	Bivalent/Poised TSS	Fetal Kidney	kidney
29	chr10:90966800-90968200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:90966800-90968200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:90966800-90968200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
32	chr10:90966800-90968200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr10:90966800-90968200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:90966800-90968200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr10:90966800-90968200	Flanking Active TSS	HMEC	breast
36	chr10:90966800-90968400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
37	chr10:90966800-90968400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:90966800-90968400	Active TSS	Brain Cingulate Gyrus	brain
39	chr10:90966800-90968400	Active TSS	Brain Substantia Nigra	brain
40	chr10:90966800-90968400	Bivalent/Poised TSS	Psoas Muscle	Psoas
41	chr10:90967000-90968200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:90967000-90968200	Flanking Bivalent TSS/Enh	Liver	Liver
43	chr10:90967000-90968200	Active TSS	Gastric	stomach
44	chr10:90967000-90968200	Enhancers	Spleen	Spleen
45	chr10:90967000-90968400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:90967000-90968400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr10:90967000-90968400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr10:90967000-90968400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr10:90967000-90968400	Active TSS	Right Atrium	heart
50	chr10:90967000-90968400	Flanking Active TSS	HUVEC	blood vessel

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