Variant report

Variant	rs12588742
Chromosome Location	chr14:24669465-24669466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24668817-24669718	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:24669441-24669491	GM12891	blood:	n/a
2	chr14:24669441-24669491	BE2_C	brain:	n/a
3	chr14:24669441-24669491	HAEpiC	amniotic membrane:	n/a
4	chr14:24669441-24669491	U87	brain:	n/a
5	chr14:24669441-24669491	ECC-1	luminal epithelium:	n/a
6	chr14:24669441-24669491	Caco-2	colon:	n/a
7	chr14:24669441-24669491	AG09309	skin:	n/a
8	chr14:24669441-24669491	PANC-1	pancreas:	n/a
9	chr14:24669441-24669491	NT2-D1	testis:	n/a
10	chr14:24669441-24669491	Hepatocyte	liver:	n/a
11	chr14:24669441-24669491	BJ	skin:	n/a
12	chr14:24669441-24669491	NHDF-neo	bronchial:	n/a
13	chr14:24669441-24669491	GM12892	blood:	n/a
14	chr14:24669441-24669491	HPAEpiC	pulmonary alveolar:	n/a
15	chr14:24669441-24669491	MCF-7	breast:	n/a
16	chr14:24669441-24669491	SK-N-MC	brain:	n/a
17	chr14:24669441-24669491	AG04449	skin:	fetal
18	chr14:24669441-24669491	GM19239	blood:	n/a
19	chr14:24669441-24669491	HCPEpiC	choroid plexus:	n/a
20	chr14:24669441-24669491	PFSK-1	brain:	n/a
21	chr14:24669441-24669491	LNCaP	prostate:	n/a
22	chr14:24669441-24669491	GM12878	blood:	n/a
23	chr14:24669441-24669491	CMK	blood:	n/a
24	chr14:24669441-24669491	H1-hESC	embryonic stem cell:	embryo
25	chr14:24669441-24669491	NHBE	bronchial:	n/a
26	chr14:24669441-24669491	AG04450	lung:	fetal
27	chr14:24669441-24669491	HIPEpiC	eye:	n/a
28	chr14:24669441-24669491	HCT-116	colon:	n/a
29	chr14:24669441-24669491	AG10803	skin:	n/a
30	chr14:24669441-24669491	HEEpiC	esophagus:	n/a
31	chr14:24669441-24669491	ProgFib	skin:	n/a
32	chr14:24669441-24669491	K562	blood:	n/a
33	chr14:24669441-24669491	HNPCEpiC	eye:	n/a
34	chr14:24669441-24669491	HepG2	liver:	n/a
35	chr14:24669441-24669491	NH-A	brain:	n/a
36	chr14:24669441-24669491	ovcar-3	ovarian:	n/a
37	chr14:24669441-24669491	PrEC	prostate:	n/a
38	chr14:24669441-24669491	T-47D	breast:	n/a
39	chr14:24669441-24669491	HL-60	blood:	n/a
40	chr14:24669441-24669491	HRE	kidney:	n/a
41	chr14:24669441-24669491	A549	lung:	n/a
42	chr14:24669441-24669491	HCM	heart:	n/a
43	chr14:24669441-24669491	HCF	heart:	n/a
44	chr14:24669441-24669491	AG09319	gingival:	n/a
45	chr14:24669441-24669491	RPTEC	kidney:	n/a
46	chr14:24669441-24669491	IMR90	lung:	fetal
47	chr14:24669441-24669491	GM06990	blood:	n/a
48	chr14:24669441-24669491	HRPEpiC	eye:	n/a
49	chr14:24669441-24669491	NB4	blood:	n/a
50	chr14:24669441-24669491	SK-N-SH_RA	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:24668234..24669903-chr14:24911019..24913097,2	MCF-7	breast:
2	chr14:24656588..24659122-chr14:24669453..24672257,2	MCF-7	breast:

No data

Variant related genes	Relation type
TM9SF1	TF binding region
TM9SF1	CpG island
ENSG00000100445	Chromatin interaction
ENSG00000196497	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1242023	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588782	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12589157	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17184526	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1885710	0.85[YRI][hapmap]
rs2234095	0.90[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234096	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2295318	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2295319	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3814815	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs55949103	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59033623	0.80[ASN][1000 genomes]
rs6573607	0.84[YRI][hapmap]
rs72694306	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72694311	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72694312	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8007272	0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24665600-24670400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:24665600-24674800	Weak transcription	Esophagus	oesophagus
3	chr14:24665800-24670600	Weak transcription	Spleen	Spleen
4	chr14:24665800-24670800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:24665800-24675000	Weak transcription	Aorta	Aorta
6	chr14:24665800-24681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:24666000-24670000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:24666000-24670400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr14:24666000-24670600	Weak transcription	Fetal Kidney	kidney
10	chr14:24666000-24670800	Weak transcription	Brain Substantia Nigra	brain
11	chr14:24666000-24670800	Weak transcription	HMEC	breast
12	chr14:24666000-24672200	Weak transcription	NHLF	lung
13	chr14:24666000-24674200	Weak transcription	Gastric	stomach
14	chr14:24666000-24674800	Weak transcription	Ovary	ovary
15	chr14:24666000-24675000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:24666000-24675800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:24666200-24670400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:24666200-24670600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr14:24666200-24670600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:24666200-24670600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr14:24666200-24670600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:24666200-24670600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:24666200-24673200	Weak transcription	Psoas Muscle	Psoas
24	chr14:24666600-24669800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr14:24666600-24670400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr14:24666600-24670400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:24666600-24670400	Weak transcription	Lung	lung
28	chr14:24666600-24670600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:24666600-24670600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:24666600-24670600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:24666600-24670600	Weak transcription	Brain Angular Gyrus	brain
32	chr14:24666600-24670600	Weak transcription	Fetal Brain Female	brain
33	chr14:24666600-24670600	Weak transcription	Fetal Lung	lung
34	chr14:24666600-24670800	Weak transcription	Primary T cells from cord blood	blood
35	chr14:24666600-24670800	Weak transcription	Thymus	Thymus
36	chr14:24666600-24672200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:24666600-24672200	Weak transcription	HSMM	muscle
38	chr14:24666600-24672200	Weak transcription	HSMMtube	muscle
39	chr14:24666600-24674200	Weak transcription	NHDF-Ad	bronchial
40	chr14:24666600-24675000	Weak transcription	Brain Germinal Matrix	brain
41	chr14:24666600-24675000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr14:24666600-24675000	Weak transcription	Right Ventricle	heart
43	chr14:24666600-24675000	Weak transcription	NH-A	brain
44	chr14:24666600-24675200	Weak transcription	HUVEC	blood vessel
45	chr14:24666600-24676000	Weak transcription	Stomach Mucosa	stomach
46	chr14:24666600-24676600	Weak transcription	Small Intestine	intestine
47	chr14:24666600-24678600	Weak transcription	Hela-S3	cervix
48	chr14:24666600-24679000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr14:24666600-24682200	Weak transcription	Fetal Heart	heart
50	chr14:24666800-24670400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links