Variant report

Variant	rs771273
Chromosome Location	chr2:7134177-7134178
allele	A/T
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	EP300	chr2:7132151-7135468	SK-N-SH	brain:	n/a	chr2:7135332-7135340 chr2:7134544-7134558 chr2:7135327-7135341 chr2:7134731-7134747
2	RAD21	chr2:7134162-7134514	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
RNF144A	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11685858	0.82[YRI][hapmap]
rs2444299	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460401	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs309309	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs309316	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309318	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs309320	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309324	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs364891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs388038	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs397865	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407427	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407798	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs436955	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs441766	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs443363	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454213	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73141632	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs771272	0.84[YRI][hapmap]

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	nsv833326	chr2:6985027-7142564	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs771273	RNF144A	cis	intralobular white matter	BrainEAC
rs771273	RNF144A	cis	thalamus	BrainEAC
rs771273	RNF144A	cis	inferior olivary nucleus	BrainEAC
rs771273	RNF144A	cis	cerebellar cortex	BrainEAC
rs771273	RNF144A	cis	brain	BrainEAC

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:7101200-7144000	Weak transcription	Aorta	Aorta
2	chr2:7101200-7154000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:7109200-7137000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:7115800-7148800	Weak transcription	Esophagus	oesophagus
5	chr2:7121200-7145400	Weak transcription	Thymus	Thymus
6	chr2:7121400-7148200	Weak transcription	Fetal Intestine Small	intestine
7	chr2:7124000-7157600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:7126600-7147600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:7126800-7141800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:7126800-7148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:7127200-7154000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:7127600-7138800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:7127600-7143600	Weak transcription	HepG2	liver
14	chr2:7131000-7167600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:7131200-7141000	Strong transcription	Primary T cells from cord blood	blood
16	chr2:7131200-7146800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:7131400-7135400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:7131400-7135600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:7131400-7150200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:7131400-7162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:7131600-7136600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr2:7131600-7137200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:7131600-7137200	Enhancers	Brain Substantia Nigra	brain
24	chr2:7131600-7154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:7131600-7154200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:7131800-7135200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:7131800-7139000	Weak transcription	Fetal Thymus	thymus
28	chr2:7132000-7134400	Enhancers	HUVEC	blood vessel
29	chr2:7132000-7135000	Enhancers	Right Ventricle	heart
30	chr2:7132000-7135200	Enhancers	Fetal Muscle Leg	muscle
31	chr2:7132000-7136200	Enhancers	Right Atrium	heart
32	chr2:7132200-7135000	Enhancers	Lung	lung
33	chr2:7132200-7135200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:7132200-7135400	Enhancers	Left Ventricle	heart
35	chr2:7132200-7135600	Enhancers	Brain Angular Gyrus	brain
36	chr2:7132200-7135800	Enhancers	Adipose Nuclei	Adipose
37	chr2:7132400-7135200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:7132400-7135400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:7132400-7135600	Enhancers	Fetal Muscle Trunk	muscle
40	chr2:7132600-7134800	Weak transcription	Fetal Brain Male	brain
41	chr2:7132600-7135000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:7132600-7135200	Enhancers	Fetal Lung	lung
43	chr2:7132600-7135400	Enhancers	Brain Germinal Matrix	brain
44	chr2:7132600-7136800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:7132600-7137400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:7132800-7134400	Weak transcription	Dnd41	blood
47	chr2:7132800-7134800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:7132800-7135400	Enhancers	Pancreas	Pancrea
49	chr2:7132800-7136000	Enhancers	Spleen	Spleen
50	chr2:7132800-7146600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links