Variant report

Variant	rs12594483
Chromosome Location	chr15:43021986-43021987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43021644-43022006	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:43021644-43022047	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:43021062-43025465	K562	blood:	n/a	n/a
4	SPI1	chr15:43021702-43022176	HL-60	blood:	n/a	chr15:43021847-43021860
5	POLR2A	chr15:43021163-43023281	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:43021976-43022026	BE2_C	brain:	n/a
2	chr15:43021976-43022026	BJ	skin:	n/a
3	chr15:43021976-43022026	PFSK-1	brain:	n/a
4	chr15:43021976-43022026	HRE	kidney:	n/a
5	chr15:43021976-43022026	HMEC	breast:	n/a
6	chr15:43021976-43022026	IMR90	lung:	fetal
7	chr15:43021976-43022026	Hepatocyte	liver:	n/a
8	chr15:43021976-43022026	A549	lung:	n/a
9	chr15:43021976-43022026	HRPEpiC	eye:	n/a
10	chr15:43021976-43022026	PrEC	prostate:	n/a
11	chr15:43021976-43022026	LNCaP	prostate:	n/a
12	chr15:43021976-43022026	SAEC	small airway:	n/a
13	chr15:43021976-43022026	AG04450	lung:	fetal
14	chr15:43021976-43022026	NB4	blood:	n/a
15	chr15:43021976-43022026	SK-N-SH_RA	brain:	n/a
16	chr15:43021976-43022026	GM06990	blood:	n/a
17	chr15:43021976-43022026	Hela-S3	cervix:	n/a
18	chr15:43021976-43022026	SK-N-SH	brain:	n/a
19	chr15:43021976-43022026	HNPCEpiC	eye:	n/a
20	chr15:43021976-43022026	HCPEpiC	choroid plexus:	n/a
21	chr15:43021976-43022026	HPAEpiC	pulmonary alveolar:	n/a
22	chr15:43021976-43022026	NHBE	bronchial:	n/a
23	chr15:43021976-43022026	PANC-1	pancreas:	n/a
24	chr15:43021976-43022026	GM12892	blood:	n/a
25	chr15:43021976-43022026	Jurkat	blood:	n/a
26	chr15:43021976-43022026	ECC-1	luminal epithelium:	n/a
27	chr15:43021976-43022026	MCF10A-Er-Src	breast:	n/a
28	chr15:43021976-43022026	ovcar-3	ovarian:	n/a
29	chr15:43021976-43022026	HUVEC	blood vessel:	n/a
30	chr15:43021976-43022026	Caco-2	colon:	n/a
31	chr15:43021976-43022026	RPTEC	kidney:	n/a
32	chr15:43021976-43022026	H1-hESC	embryonic stem cell:	embryo
33	chr15:43021976-43022026	GM12891	blood:	n/a
34	chr15:43021976-43022026	HAEpiC	amniotic membrane:	n/a
35	chr15:43021976-43022026	T-47D	breast:	n/a
36	chr15:43021976-43022026	HL-60	blood:	n/a
37	chr15:43021976-43022026	GM12878	blood:	n/a
38	chr15:43021976-43022026	HEK293	kidney:	embryo
39	chr15:43021976-43022026	ProgFib	skin:	n/a
40	chr15:43021976-43022026	HEEpiC	esophagus:	n/a
41	chr15:43021976-43022026	HCT-116	colon:	n/a
42	chr15:43021976-43022026	HRCEpiC	kidney:	n/a
43	chr15:43021976-43022026	HCF	heart:	n/a
44	chr15:43021976-43022026	HIPEpiC	eye:	n/a
45	chr15:43021976-43022026	AoSMC	blood vessel:	n/a
46	chr15:43021976-43022026	U87	brain:	n/a
47	chr15:43021976-43022026	AG04449	skin:	fetal
48	chr15:43021976-43022026	HepG2	liver:	n/a
49	chr15:43021976-43022026	AG09309	skin:	n/a
50	chr15:43021976-43022026	AG10803	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:43020195..43022907-chr15:43026273..43029275,3	MCF-7	breast:
2	chr15:43019448..43022159-chr15:43025632..43028520,2	MCF-7	breast:
3	chr15:43005044..43007388-chr15:43020446..43022660,2	K562	blood:

No data

Variant related genes	Relation type
CDAN1	TF binding region
CDAN1	CpG island
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11070374	1.00[YRI][hapmap]
rs1206698	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12102055	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12594855	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12594951	0.87[ASW][hapmap]
rs12905592	1.00[AFR][1000 genomes]
rs12906497	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12907826	1.00[AFR][1000 genomes]
rs12917018	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12917189	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs16957091	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs16957104	0.96[AFR][1000 genomes]
rs1915241	0.86[AFR][1000 genomes]
rs1995939	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2136901	0.81[AFR][1000 genomes]
rs2280048	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2412740	1.00[AFR][1000 genomes]
rs2412741	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28549876	0.92[AFR][1000 genomes]
rs3199486	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs34191150	1.00[AFR][1000 genomes]
rs35616173	1.00[AFR][1000 genomes]
rs35738819	0.96[AFR][1000 genomes]
rs3742987	0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs3742988	1.00[ASW][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4923950	0.96[AFR][1000 genomes]
rs4924690	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4994112	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap]
rs6493060	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6493061	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6493067	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6493068	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs7166373	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7166775	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7167802	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap]
rs7169009	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7169202	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7174041	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7182753	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs731984	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[AFR][1000 genomes]
rs8026233	0.92[AFR][1000 genomes]
rs8027427	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs8030587	1.00[ASW][hapmap]
rs8034447	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs8035752	1.00[ASW][hapmap]
rs8036096	1.00[ASW][hapmap]
rs8043472	1.00[ASW][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9783683	1.00[YRI][hapmap]
rs9806175	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs9944248	0.83[AFR][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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
2	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
6	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
8	chr15:43008800-43027200	Strong transcription	Lung	lung
9	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
10	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
14	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
16	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
17	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
18	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:43010000-43027600	Strong transcription	Brain Anterior Caudate	brain
22	chr15:43010000-43027600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:43010200-43027400	Strong transcription	Primary T cells from cord blood	blood
24	chr15:43010200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:43010200-43027600	Strong transcription	Ovary	ovary
26	chr15:43010200-43027800	Strong transcription	Gastric	stomach
27	chr15:43010400-43026800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:43010400-43026800	Strong transcription	Thymus	Thymus
29	chr15:43010400-43027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:43010400-43027800	Strong transcription	Placenta	Placenta
31	chr15:43011000-43026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:43011000-43026800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:43011000-43027200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:43011200-43027600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:43011400-43027600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:43011600-43022800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:43011600-43028000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:43011800-43026400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr15:43011800-43027000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:43011800-43027800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:43012000-43027200	Strong transcription	Liver	Liver
42	chr15:43012200-43026400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:43012600-43026000	Strong transcription	Dnd41	blood
44	chr15:43013800-43026000	Strong transcription	Colonic Mucosa	Colon
45	chr15:43013800-43027000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:43013800-43027400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:43014000-43027800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:43014200-43026800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:43014200-43027600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:43014200-43027800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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