Variant report

Variant	rs1418740
Chromosome Location	chr9:5887533-5887534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
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	CTCF	chr9:5887400-5887550	AG10803	skin:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:95018524..95019390-chr9:5887461..5888104,2	MCF-7	breast:
2	chr9:5886316..5888360-chr9:6049322..6051751,2	MCF-7	breast:
3	chr9:5887261..5887765-chr9:6007127..6007900,2	NB4	blood:
4	chr9:5885173..5887992-chr9:5891542..5893097,2	MCF-7	breast:
5	chr9:5885059..5887812-chr9:6005618..6008458,2	K562	blood:
6	chr9:5885881..5887710-chr9:5891218..5893485,2	K562	blood:
7	chr9:5886469..5887983-chr9:6006752..6008775,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238654	TF binding region
MLANA	TF binding region
ENSG00000183354	Chromatin interaction
ENSG00000263575	Chromatin interaction
ENSG00000120215	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733517	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10733518	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733520	1.00[CEU][hapmap]
rs10739079	1.00[CEU][hapmap]
rs10758731	1.00[CEU][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap]
rs10815301	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815302	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap]
rs16923578	1.00[CEU][hapmap]
rs186913	1.00[CEU][hapmap]
rs2150703	1.00[CEU][hapmap]
rs2225469	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2233173	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap]
rs3739649	1.00[CEU][hapmap]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap]
rs4740833	1.00[CEU][hapmap]
rs4742131	1.00[CEU][hapmap]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap]
rs7029833	1.00[CEU][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7039787	0.90[EUR][1000 genomes]
rs7042947	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7044750	1.00[CEU][hapmap]
rs7846916	0.89[ASN][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1033546	chr9:5875201-5900427	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
2	chr9:5852200-5897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:5853800-5895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:5856800-5895600	Weak transcription	Brain Substantia Nigra	brain
5	chr9:5859000-5895600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:5859000-5906600	Weak transcription	Ovary	ovary
7	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
8	chr9:5863400-5895600	Weak transcription	Fetal Intestine Small	intestine
9	chr9:5863600-5896600	Weak transcription	Pancreas	Pancrea
10	chr9:5864800-5895600	Weak transcription	Gastric	stomach
11	chr9:5870800-5895600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:5871000-5895600	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:5871000-5920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:5871200-5898400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:5877000-5895600	Weak transcription	Left Ventricle	heart
16	chr9:5877000-5896000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:5877200-5894200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:5877200-5895400	Weak transcription	Fetal Stomach	stomach
19	chr9:5877200-5895600	Weak transcription	Aorta	Aorta
20	chr9:5882200-5896200	Weak transcription	Spleen	Spleen
21	chr9:5882400-5895400	Weak transcription	Primary T cells from cord blood	blood
22	chr9:5883000-5906400	Weak transcription	Fetal Brain Male	brain
23	chr9:5884200-5888800	Enhancers	HepG2	liver
24	chr9:5884600-5910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:5885200-5891600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:5885800-5898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:5886200-5888200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:5886400-5893200	Weak transcription	Placenta	Placenta
29	chr9:5886600-5895600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:5886600-5895600	Weak transcription	Right Atrium	heart
31	chr9:5886600-5895800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:5886600-5896600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:5886600-5897200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr9:5886800-5891000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:5886800-5891400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:5886800-5891800	Weak transcription	Fetal Thymus	thymus
37	chr9:5886800-5891800	Weak transcription	Thymus	Thymus
38	chr9:5886800-5896000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:5886800-5905000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr9:5886800-5920400	Weak transcription	GM12878-XiMat	blood
41	chr9:5886800-5920600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:5886800-5922000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:5887000-5895600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr9:5887000-5895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:5887000-5921600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr9:5887200-5887600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:5887200-5887800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:5887400-5887600	Enhancers	Brain Angular Gyrus	brain
49	chr9:5887400-5896800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links