Variant report

Variant	rs2959090
Chromosome Location	chr11:45989939-45989940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45986639..45988974-chr11:45989378..45991405,2	MCF-7	breast:
2	chr11:45985864..45988587-chr11:45989343..45991964,3	K562	blood:
3	chr11:45985865..45988207-chr11:45988515..45990926,3	MCF-7	breast:
4	chr11:45988485..45990717-chr11:46014188..46017080,2	K562	blood:

Variant related genes	Relation type
ENSG00000135365	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10742774	0.87[JPT][hapmap]
rs10769176	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs10769179	0.91[ASN][1000 genomes]
rs10838533	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11038720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11038723	0.94[ASN][1000 genomes]
rs11038745	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1125290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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]
rs1996573	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2860404	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2945997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945999	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2946001	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946004	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959084	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2959087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2959091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959098	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959102	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4073513	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs4144718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237659	0.88[ASN][1000 genomes]
rs4237660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756044	0.87[JPT][hapmap]
rs4756051	0.87[JPT][hapmap]
rs4756055	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6485654	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7108028	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128184	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7130281	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926314	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7935308	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7948502	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7950336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs884668	0.82[CEU][hapmap]
rs939107	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs950105	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs953230	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	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
rs2959090	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	chr11:45957200-46004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:45957200-46004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:45967600-46004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:45970800-45990400	Weak transcription	NHDF-Ad	bronchial
6	chr11:45971000-45990000	Weak transcription	Colonic Mucosa	Colon
7	chr11:45971000-45990600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:45971000-45992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:45971200-45992400	Weak transcription	Small Intestine	intestine
10	chr11:45971400-45990800	Weak transcription	HUVEC	blood vessel
11	chr11:45971800-45991400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:45972200-45992400	Weak transcription	Psoas Muscle	Psoas
13	chr11:45975200-45991600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:45975200-45999200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:45977000-45992200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr11:45980200-45995600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:45981200-45993000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:45981400-45993400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:45981400-45995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:45981800-45993400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:45982200-46002200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:45982600-45993200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:45983000-45994000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:45983000-46002200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:45983200-45993000	Strong transcription	Fetal Intestine Large	intestine
26	chr11:45983200-45993000	Strong transcription	Fetal Stomach	stomach
27	chr11:45983200-45993600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:45983200-45993600	Strong transcription	Thymus	Thymus
29	chr11:45983600-45991400	Strong transcription	Fetal Intestine Small	intestine
30	chr11:45983600-45993000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:45984000-45990000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:45984000-45990800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:45984000-45993200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:45984000-45995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:45984400-45992800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:45985000-45993000	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:45985000-46002200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr11:45985200-45990200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:45985200-45993000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:45985200-45993000	Strong transcription	Fetal Thymus	thymus
41	chr11:45985200-45993200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:45985200-45993400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:45985200-45993800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr11:45985200-45994000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:45985400-46002600	Strong transcription	Primary B cells from cord blood	blood
46	chr11:45985600-45993000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:45985600-45993800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:45985800-45993000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:45985800-45997800	Strong transcription	Primary T cells from cord blood	blood
50	chr11:45985800-46003800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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