Variant report

Variant	rs4951477
Chromosome Location	chr1:213232555-213232556
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213232021..213235868-chr1:213239449..213242510,4	K562	blood:
2	chr1:213230752..213233029-chr1:213239159..213241284,2	K562	blood:
3	chr1:213222798..213224539-chr1:213232214..213234723,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1045868	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10735511	0.90[JPT][hapmap]
rs10746440	0.90[JPT][hapmap]
rs10779598	0.90[JPT][hapmap]
rs10864032	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10864033	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10864037	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11120070	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap]
rs11120076	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120080	0.87[ASN][1000 genomes]
rs11120082	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11120084	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120102	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11586518	0.90[JPT][hapmap]
rs12026770	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1498355	0.81[EUR][1000 genomes]
rs1566248	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002284	0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs3104207	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3738806	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4951478	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951660	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4951676	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6540774	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540776	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540777	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671019	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679510	0.86[ASN][1000 genomes]
rs6697921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7537285	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7540350	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9645358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][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	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4951477	ANGEL2	cis	Nerve Tibial	GTEx
rs4951477	RPS6KC1	cis	Artery Tibial	GTEx
rs4951477	ANGEL2	cis	parietal	SCAN
rs4951477	ANGEL2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213225200-213253400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:213225200-213254400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:213225400-213254000	Weak transcription	Aorta	Aorta
4	chr1:213225400-213254000	Weak transcription	Left Ventricle	heart
5	chr1:213225400-213256600	Weak transcription	Ovary	ovary
6	chr1:213225600-213234000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:213225600-213236000	Weak transcription	Right Atrium	heart
8	chr1:213225600-213243600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:213225600-213244000	Weak transcription	HSMM	muscle
10	chr1:213225800-213234200	Weak transcription	Primary B cells from cord blood	blood
11	chr1:213225800-213252800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:213225800-213254000	Weak transcription	Primary T cells from cord blood	blood
13	chr1:213226000-213233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:213226000-213254000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:213226200-213243800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:213226200-213252800	Weak transcription	Fetal Stomach	stomach
17	chr1:213226800-213237400	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:213227000-213254000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:213227200-213243000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:213228000-213254200	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:213228600-213244000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:213228800-213238800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:213228800-213239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:213228800-213263200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:213229400-213239000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:213229400-213254200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:213229400-213283400	Weak transcription	Hela-S3	cervix
28	chr1:213229800-213239200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:213230000-213236200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:213230200-213238800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:213230200-213239200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:213230400-213239000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:213231600-213254000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:213231800-213234600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:213232000-213232800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:213232200-213232800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:213232400-213232800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
38	chr1:213232400-213232800	ZNF genes & repeats	HepG2	liver
39	chr1:213232400-213232800	ZNF genes & repeats	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links