Variant report

Variant	rs2946001
Chromosome Location	chr11:45987634-45987635
allele	A/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	chr11:45987358-45988023	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45937002..45939512-chr11:45985947..45988260,2	MCF-7	breast:

Variant related genes	Relation type
PHF21A	TF binding region
ENSG00000121680	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10769179	0.91[ASN][1000 genomes]
rs10838533	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838535	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038720	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11038723	0.94[ASN][1000 genomes]
rs11038745	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1125290	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1125291	0.93[ASN][1000 genomes]
rs12277800	0.86[ASN][1000 genomes]
rs2945997	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945999	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2946003	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946004	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959087	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2959090	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959091	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959098	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959099	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959102	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4144718	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237659	0.88[ASN][1000 genomes]
rs4237660	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485654	0.91[ASN][1000 genomes]
rs7108028	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108186	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128184	0.99[ASN][1000 genomes]
rs7130281	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926314	0.91[ASN][1000 genomes]
rs7935308	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948502	0.91[ASN][1000 genomes]
rs7950336	0.90[AMR][1000 genomes];0.89[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:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2946001	PHF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr11:45957200-46004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:45957200-46004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:45967600-46004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:45970800-45989200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:45970800-45990400	Weak transcription	NHDF-Ad	bronchial
8	chr11:45971000-45990000	Weak transcription	Colonic Mucosa	Colon
9	chr11:45971000-45990600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:45971000-45992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:45971200-45989600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:45971200-45992400	Weak transcription	Small Intestine	intestine
13	chr11:45971400-45990800	Weak transcription	HUVEC	blood vessel
14	chr11:45971800-45991400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:45972000-45989000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:45972200-45992400	Weak transcription	Psoas Muscle	Psoas
17	chr11:45972800-45988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:45975000-45989000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:45975200-45988600	Weak transcription	Brain Substantia Nigra	brain
20	chr11:45975200-45991600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:45975200-45999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:45977000-45992200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:45977200-45989000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:45977600-45988400	Weak transcription	Brain Germinal Matrix	brain
25	chr11:45977600-45989000	Weak transcription	Spleen	Spleen
26	chr11:45980200-45987800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:45980200-45995600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:45981000-45989800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:45981200-45993000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:45981400-45993400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:45981400-45995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr11:45981800-45993400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:45982200-46002200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:45982600-45993200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:45983000-45994000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:45983000-46002200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:45983200-45993000	Strong transcription	Fetal Intestine Large	intestine
38	chr11:45983200-45993000	Strong transcription	Fetal Stomach	stomach
39	chr11:45983200-45993600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:45983200-45993600	Strong transcription	Thymus	Thymus
41	chr11:45983600-45991400	Strong transcription	Fetal Intestine Small	intestine
42	chr11:45983600-45993000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:45983800-45989200	Weak transcription	Right Ventricle	heart
44	chr11:45983800-45989200	Weak transcription	HSMM	muscle
45	chr11:45984000-45987800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:45984000-45988400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:45984000-45989000	Weak transcription	Brain Angular Gyrus	brain
48	chr11:45984000-45989000	Weak transcription	Fetal Kidney	kidney
49	chr11:45984000-45990000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:45984000-45990800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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