Variant report

Variant	rs4845402
Chromosome Location	chr1:154977929-154977930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154968418..154978887-chr1:155021582..155027516,28	MCF-7	breast:
2	chr1:154977619..154978298-chr1:154989401..154990489,4	MCF-7	breast:
3	chr1:154975922..154978346-chr1:155107900..155109707,2	MCF-7	breast:
4	chr1:154968645..154978750-chr1:155013210..155021460,25	MCF-7	breast:
5	chr1:154971203..154978007-chr1:155093683..155103687,24	MCF-7	breast:
6	chr1:154976759..154978339-chr1:155101626..155103766,2	MCF-7	breast:
7	chr1:154976508..154978932-chr1:155009683..155011817,3	MCF-7	breast:
8	chr1:154971009..154978300-chr1:155033602..155036845,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232093	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1061122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908443	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264302	1.00[JPT][hapmap]
rs11264303	1.00[JPT][hapmap]
rs11465207	1.00[CHB][hapmap]
rs11582128	1.00[JPT][hapmap]
rs12058480	1.00[CHB][hapmap]
rs1218554	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1218584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1218585	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1218587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1218589	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12760148	1.00[CHB][hapmap]
rs1611770	1.00[JPT][hapmap]
rs1611772	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878412	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845396	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845700	0.85[CEU][hapmap]
rs6660884	1.00[JPT][hapmap]
rs6682335	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs906596	1.00[CHB][hapmap]
rs906597	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
4	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4845402	ANXA9	cis	cerebellum	SCAN
rs4845402	PIP5K1A	cis	cerebellum	SCAN
rs4845402	LCE1F	cis	cerebellum	SCAN
rs4845402	MTX1	cis	parietal	SCAN
rs4845402	LENEP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154975400-154978200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr1:154975800-154978200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:154976000-154978200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:154976400-154978000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr1:154976400-154988800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:154976600-154978000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:154976600-154978000	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr1:154976600-154978000	Flanking Active TSS	Lung	lung
9	chr1:154976600-154978200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:154976600-154978600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:154976600-154979600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr1:154976600-154984400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr1:154976800-154978000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:154976800-154978000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
15	chr1:154976800-154978400	Flanking Active TSS	A549	lung
16	chr1:154976800-154978600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154976800-154979000	Transcr. at gene 5' and 3'	NHEK	skin
18	chr1:154976800-154980600	Enhancers	Spleen	Spleen
19	chr1:154976800-154980800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr1:154976800-154981000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:154976800-154981600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:154977000-154978200	Enhancers	Ovary	ovary
23	chr1:154977000-154979000	Enhancers	Fetal Brain Female	brain
24	chr1:154977000-154986400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:154977200-154978000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:154977200-154978000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:154977200-154978000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:154977200-154978200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:154977200-154978200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:154977200-154978200	Enhancers	Fetal Heart	heart
31	chr1:154977200-154978600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:154977200-154978600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:154977200-154978800	Genic enhancers	Fetal Stomach	stomach
34	chr1:154977200-154979000	Enhancers	HUVEC	blood vessel
35	chr1:154977200-154979200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:154977200-154979400	Enhancers	Small Intestine	intestine
37	chr1:154977200-154980200	Enhancers	Fetal Lung	lung
38	chr1:154977200-154980400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:154977200-154980800	Enhancers	Fetal Muscle Leg	muscle
40	chr1:154977400-154978000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:154977400-154978200	Enhancers	NHLF	lung
42	chr1:154977400-154978600	Enhancers	NH-A	brain
43	chr1:154977400-154979400	Enhancers	Placenta	Placenta
44	chr1:154977400-154979600	Enhancers	HepG2	liver
45	chr1:154977400-154980600	Enhancers	Psoas Muscle	Psoas
46	chr1:154977400-154980800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:154977400-154980800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:154977400-154981000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:154977400-154981000	Enhancers	Right Atrium	heart
50	chr1:154977400-154981200	Enhancers	Left Ventricle	heart

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