Variant report

Variant	rs11038720
Chromosome Location	chr11:45968661-45968662
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45967979..45970014-chr11:45973692..45975912,2	K562	blood:
2	chr11:45967819..45970756-chr11:46009123..46011676,2	K562	blood:

Variant related genes	Relation type
ENSG00000135365	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10742774	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs10769176	0.85[CEU][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs10769179	0.83[ASN][1000 genomes]
rs10838533	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10838535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11038723	0.94[ASN][1000 genomes]
rs11038745	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1125290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1125291	0.85[ASN][1000 genomes]
rs1996573	0.82[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs2860404	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs2945997	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945999	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]
rs2946001	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2946003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2946004	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2959084	0.87[JPT][hapmap]
rs2959087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959090	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]
rs2959091	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]
rs2959098	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2959101	0.85[CHD][hapmap]
rs2959102	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073513	0.87[JPT][hapmap]
rs4144718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4237659	0.81[ASN][1000 genomes]
rs4237660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4756044	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs4756051	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4756055	0.87[JPT][hapmap]
rs6485654	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7108028	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7108186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7128184	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs7130281	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7926314	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7935308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7948502	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs7950336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7950391	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs884668	0.81[CEU][hapmap]
rs939107	0.82[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs950105	0.87[JPT][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
rs11038720	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	chr11:45945200-45969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:45952400-45996200	Weak transcription	Stomach Mucosa	stomach
3	chr11:45953000-45988600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:45953200-45972600	Strong transcription	Fetal Intestine Large	intestine
5	chr11:45953200-45975400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:45954000-45978800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:45954200-45969800	Weak transcription	HUVEC	blood vessel
8	chr11:45957200-45969400	Weak transcription	Colonic Mucosa	Colon
9	chr11:45957200-46004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:45957200-46004400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:45957600-45970600	Weak transcription	Small Intestine	intestine
12	chr11:45957600-45986400	Weak transcription	HMEC	breast
13	chr11:45957800-45969000	Weak transcription	Pancreas	Pancrea
14	chr11:45957800-45986400	Weak transcription	NHEK	skin
15	chr11:45958600-45979000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:45958800-45979000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:45959800-45969000	Weak transcription	Gastric	stomach
18	chr11:45960000-45970000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:45960200-45971400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:45960400-45986600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:45961400-45975400	Strong transcription	Placenta	Placenta
22	chr11:45962000-45978800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:45962200-45977200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:45962200-45978400	Strong transcription	Primary T cells from cord blood	blood
25	chr11:45962400-45975600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:45962600-45975200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr11:45962600-45979200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:45962800-45969600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:45962800-45970800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:45963000-45969000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:45963000-45971400	Strong transcription	Spleen	Spleen
32	chr11:45963000-45971400	Strong transcription	Osteobl	bone
33	chr11:45963000-45975200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr11:45963000-45975200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr11:45963000-45977400	Strong transcription	Primary B cells from cord blood	blood
36	chr11:45963200-45971800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr11:45963200-45974000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:45963200-45974200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:45963200-45977600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:45963400-45971200	Strong transcription	Colon Smooth Muscle	Colon
41	chr11:45963400-45971400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:45963400-45975400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:45963600-45975800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:45963800-45970200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:45963800-45970400	Strong transcription	Brain Anterior Caudate	brain
46	chr11:45964000-45975000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:45964400-45974000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:45964800-45969200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:45964800-45972000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:45965000-45970200	Strong transcription	Brain Hippocampus Middle	brain

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