Variant report

Variant	rs2946004
Chromosome Location	chr11:45997805-45997806
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	chr11:45997545-45997917	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45899726..45902315-chr11:45996941..45999150,2	MCF-7	breast:
2	chr11:45997750..46001916-chr11:46003160..46008009,7	K562	blood:

Variant related genes	Relation type
PHF21A	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10769179	0.91[ASN][1000 genomes]
rs10838533	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838535	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038720	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11038723	0.94[ASN][1000 genomes]
rs11038745	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1125290	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1125291	0.93[ASN][1000 genomes]
rs12277800	0.86[ASN][1000 genomes]
rs2945997	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945999	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2946001	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946003	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959087	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2959090	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959098	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959099	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959102	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144718	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237659	0.88[ASN][1000 genomes]
rs4237660	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485654	0.91[ASN][1000 genomes]
rs7108028	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108186	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128184	0.99[ASN][1000 genomes]
rs7130281	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926314	0.91[ASN][1000 genomes]
rs7935308	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948502	0.91[ASN][1000 genomes]
rs7950336	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950391	0.91[ASN][1000 genomes]
rs939107	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523952	chr11:45983385-46028281	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv38731	chr11:45993457-45998686	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2946004	PHF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45957200-46004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:45957200-46004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:45967600-46004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:45975200-45999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:45982200-46002200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:45983000-46002200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr11:45985000-46002200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:45985400-46002600	Strong transcription	Primary B cells from cord blood	blood
9	chr11:45985800-46003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:45987000-46004000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:45987200-46000800	Weak transcription	NHEK	skin
12	chr11:45987600-46004600	Weak transcription	Gastric	stomach
13	chr11:45988400-46004400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:45989400-46000000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:45989800-46000000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:45990000-46000000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:45990400-46000600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:45990400-46001600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:45990800-46000000	Weak transcription	NH-A	brain
20	chr11:45991000-46004400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:45991000-46004400	Weak transcription	A549	lung
22	chr11:45991800-46003600	Weak transcription	Brain Germinal Matrix	brain
23	chr11:45992200-46004400	Weak transcription	HMEC	breast
24	chr11:45992600-46000000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:45992600-46003600	Weak transcription	Fetal Brain Male	brain
26	chr11:45992800-45998400	Weak transcription	GM12878-XiMat	blood
27	chr11:45992800-45999400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:45992800-45999800	Weak transcription	HepG2	liver
29	chr11:45992800-46000000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr11:45992800-46000000	Weak transcription	Fetal Lung	lung
31	chr11:45992800-46001200	Weak transcription	Right Ventricle	heart
32	chr11:45992800-46003600	Weak transcription	Brain Angular Gyrus	brain
33	chr11:45992800-46004200	Weak transcription	HSMM	muscle
34	chr11:45992800-46004600	Weak transcription	Fetal Kidney	kidney
35	chr11:45993000-45998200	Weak transcription	Adipose Nuclei	Adipose
36	chr11:45993000-45999600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:45993000-45999600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:45993000-45999600	Weak transcription	Fetal Brain Female	brain
39	chr11:45993000-45999800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:45993000-45999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:45993000-45999800	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:45993000-46000000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:45993000-46000000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:45993000-46000000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:45993000-46000000	Weak transcription	Brain Substantia Nigra	brain
46	chr11:45993000-46000000	Weak transcription	Fetal Thymus	thymus
47	chr11:45993000-46000000	Weak transcription	Ovary	ovary
48	chr11:45993000-46000000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:45993000-46000000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr11:45993000-46000600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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