Variant report

Variant	rs1469952
Chromosome Location	chr2:11917519-11917520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:11917480-11917630	GM12865	blood:	n/a	n/a
2	MYC	chr2:11917494-11917942	NB4	blood:	n/a	n/a
3	MAX	chr2:11917426-11917977	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:11917490-11917540	ovcar-3	ovarian:	n/a
2	chr2:11917490-11917540	NT2-D1	testis:	n/a
3	chr2:11917490-11917540	HNPCEpiC	eye:	n/a
4	chr2:11917490-11917540	BJ	skin:	n/a
5	chr2:11917490-11917540	SKMC	muscle:	n/a
6	chr2:11917490-11917540	MCF-7	breast:	n/a
7	chr2:11917490-11917540	HMEC	breast:	n/a
8	chr2:11917490-11917540	GM12892	blood:	n/a
9	chr2:11917490-11917540	PFSK-1	brain:	n/a
10	chr2:11917490-11917540	HepG2	liver:	n/a
11	chr2:11917490-11917540	HL-60	blood:	n/a
12	chr2:11917490-11917540	T-47D	breast:	n/a
13	chr2:11917490-11917540	AG10803	skin:	n/a
14	chr2:11917490-11917540	HIPEpiC	eye:	n/a
15	chr2:11917490-11917540	AG09309	skin:	n/a
16	chr2:11917490-11917540	AG04450	lung:	fetal
17	chr2:11917490-11917540	AG09319	gingival:	n/a
18	chr2:11917490-11917540	HAEpiC	amniotic membrane:	n/a
19	chr2:11917490-11917540	GM06990	blood:	n/a
20	chr2:11917490-11917540	NHDF-neo	bronchial:	n/a
21	chr2:11917490-11917540	Jurkat	blood:	n/a
22	chr2:11917490-11917540	HCPEpiC	choroid plexus:	n/a
23	chr2:11917490-11917540	MCF10A-Er-Src	breast:	n/a
24	chr2:11917490-11917540	AG04449	skin:	fetal
25	chr2:11917490-11917540	HUVEC	blood vessel:	n/a
26	chr2:11917490-11917540	HCF	heart:	n/a
27	chr2:11917490-11917540	NB4	blood:	n/a
28	chr2:11917490-11917540	BE2_C	brain:	n/a
29	chr2:11917490-11917540	SAEC	small airway:	n/a
30	chr2:11917490-11917540	PANC-1	pancreas:	n/a
31	chr2:11917490-11917540	RPTEC	kidney:	n/a
32	chr2:11917490-11917540	LNCaP	prostate:	n/a
33	chr2:11917490-11917540	GM12878	blood:	n/a
34	chr2:11917490-11917540	HRCEpiC	kidney:	n/a
35	chr2:11917490-11917540	SK-N-SH_RA	brain:	n/a
36	chr2:11917490-11917540	PrEC	prostate:	n/a
37	chr2:11917490-11917540	Hepatocyte	liver:	n/a
38	chr2:11917490-11917540	HPAEpiC	pulmonary alveolar:	n/a
39	chr2:11917490-11917540	IMR90	lung:	fetal
40	chr2:11917490-11917540	HCT-116	colon:	n/a
41	chr2:11917490-11917540	HEK293	kidney:	embryo
42	chr2:11917490-11917540	ProgFib	skin:	n/a
43	chr2:11917490-11917540	CMK	blood:	n/a
44	chr2:11917490-11917540	HCM	heart:	n/a
45	chr2:11917490-11917540	NH-A	brain:	n/a
46	chr2:11917490-11917540	K562	blood:	n/a
47	chr2:11917490-11917540	GM12891	blood:	n/a
48	chr2:11917490-11917540	ECC-1	luminal epithelium:	n/a
49	chr2:11917490-11917540	H1-hESC	embryonic stem cell:	embryo
50	chr2:11917490-11917540	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11885343..11888558-chr2:11916972..11921085,4	K562	blood:

No data

Variant related genes	Relation type
LPIN1	TF binding region
LPIN1	CpG island
ENSG00000134324	Chromatin interaction
ENSG00000230790	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1006538	0.92[ASN][1000 genomes]
rs10169802	0.85[ASN][1000 genomes]
rs10192566	0.85[ASN][1000 genomes]
rs10205312	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205400	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207506	0.84[ASN][1000 genomes]
rs10208679	0.84[ASN][1000 genomes]
rs10209969	0.92[ASN][1000 genomes]
rs11676086	0.84[ASN][1000 genomes]
rs11693809	0.85[ASN][1000 genomes]
rs11897144	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407101	0.90[ASN][1000 genomes]
rs13409154	0.84[ASN][1000 genomes]
rs13412852	0.94[ASN][1000 genomes]
rs17603420	0.90[ASN][1000 genomes]
rs2278513	1.00[ASN][1000 genomes]
rs2358041	0.94[ASN][1000 genomes]
rs2358042	0.94[ASN][1000 genomes]
rs2358126	0.89[ASN][1000 genomes]
rs4076055	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4129757	0.91[ASN][1000 genomes]
rs4315495	0.84[ASN][1000 genomes]
rs62113306	0.82[ASN][1000 genomes]
rs6717910	0.99[ASN][1000 genomes]
rs6731096	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6757892	0.91[ASN][1000 genomes]
rs72773994	0.92[ASN][1000 genomes]
rs7561070	0.91[ASN][1000 genomes]
rs7595221	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7607755	0.91[ASN][1000 genomes]
rs873358	0.84[ASN][1000 genomes]
rs893342	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11895000-11918200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:11900600-11918000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:11901800-11918600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:11905200-11919000	Weak transcription	Stomach Mucosa	stomach
5	chr2:11906400-11924600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:11906600-11924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:11906800-11924600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:11908000-11919000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:11908600-11917600	Strong transcription	K562	blood
10	chr2:11909000-11919000	Strong transcription	HMEC	breast
11	chr2:11910000-11918400	Strong transcription	Thymus	Thymus
12	chr2:11911800-11918200	Weak transcription	Small Intestine	intestine
13	chr2:11912000-11919000	Weak transcription	A549	lung
14	chr2:11912400-11917600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:11912400-11918200	Weak transcription	Colonic Mucosa	Colon
16	chr2:11912400-11919200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:11912600-11918400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11912600-11918400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:11912600-11920400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:11913600-11919000	Weak transcription	Brain Substantia Nigra	brain
21	chr2:11914000-11919600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:11914600-11918600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:11914800-11918400	Weak transcription	Primary B cells from cord blood	blood
24	chr2:11914800-11919200	Weak transcription	Fetal Brain Male	brain
25	chr2:11914800-11920200	Weak transcription	Fetal Lung	lung
26	chr2:11915000-11918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:11915000-11918400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:11915000-11918600	Weak transcription	Fetal Brain Female	brain
29	chr2:11915000-11918800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:11915000-11919200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:11915000-11919200	Weak transcription	Right Ventricle	heart
32	chr2:11915000-11923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:11915200-11918400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:11915200-11919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:11915200-11919200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:11915200-11919600	Weak transcription	Ovary	ovary
37	chr2:11915400-11918400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:11915400-11918800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:11915400-11919000	Weak transcription	Fetal Heart	heart
40	chr2:11915400-11919200	Weak transcription	HSMMtube	muscle
41	chr2:11915600-11917600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:11915600-11918000	Strong transcription	Hela-S3	cervix
43	chr2:11915600-11919200	Weak transcription	Brain Germinal Matrix	brain
44	chr2:11915600-11919400	Enhancers	Fetal Intestine Large	intestine
45	chr2:11915800-11918200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr2:11915800-11918400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:11915800-11918400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:11915800-11918800	Strong transcription	Liver	Liver
49	chr2:11915800-11919000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:11915800-11919000	Weak transcription	NH-A	brain

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