Variant report

Variant	rs4845606
Chromosome Location	chr1:151801951-151801952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:151801378-151802010	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr1:151801371-151801956	U87	brain:	n/a	n/a
3	REST	chr1:151801390-151801971	ECC-1	luminal epithelium:	n/a	n/a
4	REST	chr1:151801310-151802106	PFSK-1	brain:	n/a	n/a
5	REST	chr1:151801361-151802444	MCF-7	breast:	n/a	n/a
6	REST	chr1:151801333-151802311	PFSK-1	brain:	n/a	n/a
7	REST	chr1:151801396-151802208	K562	blood:	n/a	n/a
8	REST	chr1:151801413-151801952	A549	lung:	n/a	n/a
9	REST	chr1:151801340-151801990	SK-N-SH	brain:	n/a	n/a
10	REST	chr1:151801400-151801954	U87	brain:	n/a	n/a
11	REST	chr1:151801415-151802058	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr1:151801355-151802511	MCF-7	breast:	n/a	n/a
13	REST	chr1:151801418-151801995	GM12878	blood:	n/a	n/a
14	REST	chr1:151801418-151802082	HL-60	blood:	n/a	n/a
15	REST	chr1:151801346-151802211	HL-60	blood:	n/a	n/a
16	REST	chr1:151801392-151802072	ECC-1	luminal epithelium:	n/a	n/a
17	REST	chr1:151801331-151802019	PFSK-1	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151762059..151766604-chr1:151800169..151809078,15	MCF-7	breast:
2	chr1:151767476..151771496-chr1:151798617..151803699,6	MCF-7	breast:
3	chr1:151776821..151779307-chr1:151800357..151803039,2	MCF-7	breast:
4	chr1:151772358..151773986-chr1:151801710..151803954,2	MCF-7	breast:
5	chr1:151800004..151802525-chr1:151803685..151806343,2	MCF-7	breast:
6	chr1:151795588..151797929-chr1:151801830..151803659,3	MCF-7	breast:
7	chr1:151795791..151798042-chr1:151801058..151802708,2	K562	blood:
8	chr1:151798062..151799748-chr1:151801551..151803345,2	K562	blood:
9	chr1:151801687..151803757-chr3:196651344..196653748,2	MCF-7	breast:
10	chr1:151680409..151681994-chr1:151800376..151802986,2	K562	blood:

No data

Variant related genes	Relation type
RORC	TF binding region
ENSG00000143365	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000213171	Chromatin interaction
ENSG00000269489	Chromatin interaction
ENSG00000182134	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11204894	1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs11582525	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126984	1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes]
rs3790515	0.82[JPT][hapmap]
rs3811417	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3811418	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3811419	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845602	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72692781	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72692783	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7540799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4845606	S100A16	cis	cerebellum	SCAN
rs4845606	S100A10	cis	parietal	SCAN
rs4845606	C1orf51	cis	parietal	SCAN
rs4845606	SCNM1	cis	parietal	SCAN
rs4845606	PSMD4	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:151796200-151803600	Enhancers	Fetal Muscle Trunk	muscle
3	chr1:151797000-151803600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:151797800-151803800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:151798400-151807000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:151798800-151804400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:151799000-151807800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:151799600-151802000	Flanking Active TSS	Fetal Thymus	thymus
9	chr1:151799600-151803200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:151799800-151803200	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:151799800-151803400	Enhancers	Fetal Muscle Leg	muscle
12	chr1:151799800-151803800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:151799800-151804000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr1:151800000-151802600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr1:151800000-151803600	Enhancers	Spleen	Spleen
16	chr1:151800000-151804200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:151800000-151806400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr1:151800200-151803400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:151800200-151803600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:151800200-151804000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:151800400-151802000	Genic enhancers	Pancreas	Pancrea
22	chr1:151800400-151802400	Enhancers	Placenta	Placenta
23	chr1:151800400-151802800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:151800400-151803400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:151800400-151804800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:151800600-151802000	Enhancers	Fetal Heart	heart
27	chr1:151800600-151802200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:151800600-151802200	Enhancers	GM12878-XiMat	blood
29	chr1:151800600-151802400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:151800600-151802400	Enhancers	Adipose Nuclei	Adipose
31	chr1:151800600-151802400	Enhancers	Fetal Intestine Large	intestine
32	chr1:151800600-151802400	Bivalent Enhancer	Fetal Stomach	stomach
33	chr1:151800600-151802800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:151800600-151802800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:151800600-151803400	Enhancers	Lung	lung
36	chr1:151800600-151803800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr1:151800600-151804400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:151800800-151802200	Enhancers	Primary B cells from cord blood	blood
39	chr1:151800800-151802400	Enhancers	Fetal Kidney	kidney
40	chr1:151800800-151802400	Enhancers	HUVEC	blood vessel
41	chr1:151800800-151802600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:151800800-151802600	Enhancers	HMEC	breast
43	chr1:151800800-151802800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:151800800-151802800	Enhancers	Brain Germinal Matrix	brain
45	chr1:151800800-151802800	Enhancers	Brain Substantia Nigra	brain
46	chr1:151800800-151803000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:151800800-151803400	Enhancers	Left Ventricle	heart
48	chr1:151800800-151803400	Enhancers	Stomach Mucosa	stomach
49	chr1:151800800-151803800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:151801000-151802000	Enhancers	Primary T helper cells PMA-I stimulated	--

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