Variant report

Variant	rs2959102
Chromosome Location	chr11:45975597-45975598
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10769179	0.84[ASN][1000 genomes]
rs10838533	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10838535	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11038720	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11038723	0.95[ASN][1000 genomes]
rs11038745	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1125290	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1125291	0.86[ASN][1000 genomes]
rs2945997	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945999	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2946001	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2946003	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2946004	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959087	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959090	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959091	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959098	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959099	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4144718	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237659	0.82[ASN][1000 genomes]
rs4237660	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485654	0.84[ASN][1000 genomes]
rs7108028	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7108186	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7128184	0.92[ASN][1000 genomes]
rs7130281	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7926314	0.84[ASN][1000 genomes]
rs7935308	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7948502	0.84[ASN][1000 genomes]
rs7950336	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950391	0.84[ASN][1000 genomes]
rs939107	0.94[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	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2959102	PHF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45952400-45996200	Weak transcription	Stomach Mucosa	stomach
2	chr11:45953000-45988600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:45954000-45978800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr11:45957200-46004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:45957200-46004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:45957600-45986400	Weak transcription	HMEC	breast
7	chr11:45957800-45986400	Weak transcription	NHEK	skin
8	chr11:45958600-45979000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:45958800-45979000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:45960400-45986600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:45962000-45978800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:45962200-45977200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:45962200-45978400	Strong transcription	Primary T cells from cord blood	blood
14	chr11:45962400-45975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:45962600-45979200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:45963000-45977400	Strong transcription	Primary B cells from cord blood	blood
17	chr11:45963200-45977600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:45963600-45975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:45965800-45977200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:45966400-45979000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr11:45967600-46004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:45967800-45977600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr11:45968000-45985800	Weak transcription	K562	blood
24	chr11:45969000-45976600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:45969600-45975600	Strong transcription	Hela-S3	cervix
26	chr11:45969800-45983400	Weak transcription	Fetal Heart	heart
27	chr11:45970400-45985200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:45970600-45983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:45970600-45986200	Weak transcription	NHLF	lung
30	chr11:45970600-45986600	Weak transcription	Pancreas	Pancrea
31	chr11:45970600-45986800	Weak transcription	HepG2	liver
32	chr11:45970800-45975600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:45970800-45983000	Weak transcription	Fetal Brain Female	brain
34	chr11:45970800-45989200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:45970800-45990400	Weak transcription	NHDF-Ad	bronchial
36	chr11:45971000-45977600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:45971000-45983400	Weak transcription	Right Ventricle	heart
38	chr11:45971000-45985800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:45971000-45986800	Weak transcription	Gastric	stomach
40	chr11:45971000-45990000	Weak transcription	Colonic Mucosa	Colon
41	chr11:45971000-45990600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:45971000-45992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:45971200-45985200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:45971200-45986600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:45971200-45989600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:45971200-45992400	Weak transcription	Small Intestine	intestine
47	chr11:45971400-45977200	Weak transcription	Spleen	Spleen
48	chr11:45971400-45981600	Weak transcription	Fetal Kidney	kidney
49	chr11:45971400-45990800	Weak transcription	HUVEC	blood vessel
50	chr11:45971600-45981000	Weak transcription	A549	lung

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