Variant report

Variant	rs2054390
Chromosome Location	chr11:10550251-10550252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:10550082..10553172-chr11:10561371..10563862,3	MCF-7	breast:
2	chr11:10548650..10551746-chr11:10552608..10557430,5	K562	blood:
3	chr11:10544820..10548586-chr11:10548781..10551121,4	K562	blood:
4	chr11:10386948..10389618-chr11:10548931..10550631,2	K562	blood:
5	chr11:10546252..10548492-chr11:10548781..10550979,2	K562	blood:

Variant related genes	Relation type
ENSG00000110315	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1047730	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11602469	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11604691	1.00[ASN][1000 genomes]
rs11607008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11826750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12275930	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12290357	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12294022	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4909938	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4909940	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909941	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4910149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910151	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7123581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128848	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131507	0.88[ASN][1000 genomes]
rs73411920	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929890	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7938782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10501600-10550600	Weak transcription	Small Intestine	intestine
2	chr11:10502600-10560800	Weak transcription	Fetal Brain Male	brain
3	chr11:10522400-10560800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:10525800-10555600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr11:10526400-10551800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:10526400-10561600	Weak transcription	Colonic Mucosa	Colon
7	chr11:10528400-10550600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:10528400-10555800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:10533200-10552000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:10533200-10561600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:10533200-10561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:10533400-10561400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:10533800-10557400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:10535600-10556200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:10536400-10555600	Strong transcription	Primary B cells from cord blood	blood
16	chr11:10538200-10561600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:10538400-10550600	Weak transcription	Pancreas	Pancrea
18	chr11:10538400-10561600	Weak transcription	Esophagus	oesophagus
19	chr11:10538400-10561600	Weak transcription	Lung	lung
20	chr11:10539400-10555800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:10540200-10553400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:10540200-10555400	Strong transcription	Liver	Liver
23	chr11:10540200-10555600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:10540400-10551600	Strong transcription	Dnd41	blood
25	chr11:10540400-10553600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:10540600-10552000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr11:10540600-10552200	Strong transcription	Adipose Nuclei	Adipose
28	chr11:10540600-10554600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr11:10540600-10555600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:10540800-10555200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:10541000-10551800	Strong transcription	Primary T cells from cord blood	blood
32	chr11:10541400-10561600	Weak transcription	Fetal Heart	heart
33	chr11:10541600-10561400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:10541600-10562000	Weak transcription	Gastric	stomach
35	chr11:10542200-10561600	Weak transcription	Fetal Stomach	stomach
36	chr11:10543400-10551400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:10543400-10552600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:10544000-10551400	Strong transcription	Placenta	Placenta
39	chr11:10544200-10561400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:10544600-10553200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr11:10544800-10552000	Enhancers	HUVEC	blood vessel
42	chr11:10544800-10552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:10544800-10554400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:10545000-10550400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr11:10545000-10550400	Weak transcription	HSMM	muscle
46	chr11:10545600-10550600	Weak transcription	Fetal Kidney	kidney
47	chr11:10545600-10554600	Weak transcription	HepG2	liver
48	chr11:10546400-10550400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:10546400-10555800	Strong transcription	Fetal Thymus	thymus
50	chr11:10546600-10555400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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