Variant report

Variant	rs1475766
Chromosome Location	chr1:155981489-155981490
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155981430-155981606	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155976501..155978823-chr1:155979860..155982073,3	MCF-7	breast:
2	chr1:155978931..155981805-chr1:155987502..155989827,3	MCF-7	breast:
3	chr1:155979319..155982238-chr1:156049150..156050811,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10908486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111102	0.82[YRI][hapmap]
rs11577179	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582305	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12032631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043212	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12128541	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17381047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17385065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966243	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2095402	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297792	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2364400	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364401	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2886070	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34126883	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34444588	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34995046	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4330912	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4661079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668204	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517202	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1475766	ROBLD3	cis	parietal	SCAN
rs1475766	SPRR3	cis	parietal	SCAN
rs1475766	PRUNE	cis	cerebellum	SCAN
rs1475766	RIT1	cis	cerebellum	SCAN
rs1475766	SNX27	cis	parietal	SCAN
rs1475766	UBQLN4	trans	parietal	SCAN
rs1475766	YY1AP1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155973800-155989400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155976000-155989600	Strong transcription	Fetal Stomach	stomach
3	chr1:155976200-155988800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:155976600-155982400	Strong transcription	Spleen	Spleen
5	chr1:155976600-155985000	Strong transcription	Lung	lung
6	chr1:155976600-155985400	Strong transcription	Thymus	Thymus
7	chr1:155976600-155988400	Strong transcription	Liver	Liver
8	chr1:155976600-155988400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:155976600-155988600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:155976600-155988800	Strong transcription	Fetal Intestine Small	intestine
11	chr1:155976600-155989200	Strong transcription	Fetal Intestine Large	intestine
12	chr1:155976600-155989400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:155976800-155985000	Strong transcription	Fetal Brain Female	brain
14	chr1:155976800-155985400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:155976800-155989400	Strong transcription	Fetal Thymus	thymus
16	chr1:155976800-155989600	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:155977200-155983400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:155977200-155987000	Weak transcription	Fetal Heart	heart
19	chr1:155977200-155989200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:155978000-155983800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:155978200-155982200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:155978200-155982200	Strong transcription	Esophagus	oesophagus
23	chr1:155978200-155982200	Strong transcription	Pancreas	Pancrea
24	chr1:155978200-155983400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:155978200-155983400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:155978200-155985000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:155978200-155985000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:155978200-155985000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:155978200-155985000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:155978200-155985000	Strong transcription	Brain Substantia Nigra	brain
31	chr1:155978200-155985000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:155978200-155985200	Strong transcription	Aorta	Aorta
33	chr1:155978200-155985400	Strong transcription	Adipose Nuclei	Adipose
34	chr1:155978200-155985400	Strong transcription	NHLF	lung
35	chr1:155978200-155986000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:155978200-155987000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:155978200-155988200	Strong transcription	Colon Smooth Muscle	Colon
38	chr1:155978200-155988200	Strong transcription	Left Ventricle	heart
39	chr1:155978200-155988600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:155978200-155989000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:155978200-155989200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:155978200-155989200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:155978200-155989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:155978200-155989200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:155978200-155989600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:155978200-155989600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:155978200-155989600	Strong transcription	Placenta	Placenta
48	chr1:155978400-155985000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:155978400-155985000	Strong transcription	K562	blood
50	chr1:155978400-155985200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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