Variant report

Variant	rs2945999
Chromosome Location	chr11:45982957-45982958
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45981105..45984613-chr11:45985057..45988704,3	K562	blood:
2	chr11:45957153..45959424-chr11:45981539..45983603,2	K562	blood:

Variant related genes	Relation type
ENSG00000135365	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10742774	0.81[JPT][hapmap]
rs10769176	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs10838533	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10838535	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11038720	0.85[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11038745	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1125290	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2860404	0.81[JPT][hapmap]
rs2945997	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2946001	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2946003	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2946004	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2959084	0.81[JPT][hapmap]
rs2959087	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2959090	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2959091	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2959098	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959099	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959101	0.84[MEX][hapmap]
rs2959102	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4073513	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs4144718	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4237660	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4756044	0.81[JPT][hapmap]
rs4756051	0.81[JPT][hapmap]
rs4756055	0.81[JPT][hapmap]
rs6485654	0.85[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs7108028	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7108186	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7128184	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs7130281	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7926314	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs7935308	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7948502	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs7950336	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7950391	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs939107	0.82[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs950105	0.81[JPT][hapmap]
rs953230	0.83[MEX][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	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
rs2945999	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	chr11:45957200-46004400	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	chr11:45957600-45986400	Weak transcription	HMEC	breast
6	chr11:45957800-45986400	Weak transcription	NHEK	skin
7	chr11:45960400-45986600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:45967600-46004600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:45968000-45985800	Weak transcription	K562	blood
10	chr11:45969800-45983400	Weak transcription	Fetal Heart	heart
11	chr11:45970400-45985200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:45970600-45983400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:45970600-45986200	Weak transcription	NHLF	lung
14	chr11:45970600-45986600	Weak transcription	Pancreas	Pancrea
15	chr11:45970600-45986800	Weak transcription	HepG2	liver
16	chr11:45970800-45983000	Weak transcription	Fetal Brain Female	brain
17	chr11:45970800-45989200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:45970800-45990400	Weak transcription	NHDF-Ad	bronchial
19	chr11:45971000-45983400	Weak transcription	Right Ventricle	heart
20	chr11:45971000-45985800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:45971000-45986800	Weak transcription	Gastric	stomach
22	chr11:45971000-45990000	Weak transcription	Colonic Mucosa	Colon
23	chr11:45971000-45990600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:45971000-45992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:45971200-45985200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:45971200-45986600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:45971200-45989600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:45971200-45992400	Weak transcription	Small Intestine	intestine
29	chr11:45971400-45990800	Weak transcription	HUVEC	blood vessel
30	chr11:45971600-45986600	Weak transcription	Fetal Brain Male	brain
31	chr11:45971800-45991400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr11:45972000-45983200	Weak transcription	Esophagus	oesophagus
33	chr11:45972000-45986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:45972000-45986800	Weak transcription	Aorta	Aorta
35	chr11:45972000-45989000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:45972200-45992400	Weak transcription	Psoas Muscle	Psoas
37	chr11:45972400-45983200	Weak transcription	Lung	lung
38	chr11:45972400-45983400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:45972600-45983200	Weak transcription	HSMMtube	muscle
40	chr11:45972600-45986600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:45972800-45986000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:45972800-45988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:45973000-45983200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:45973200-45983200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:45974000-45983000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:45974000-45986600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:45974200-45986000	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:45974400-45983000	Weak transcription	Fetal Thymus	thymus
49	chr11:45975000-45983600	Weak transcription	NH-A	brain
50	chr11:45975000-45985400	Weak transcription	Duodenum Mucosa	Duodenum

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