Variant report

Variant	rs17154142
Chromosome Location	chr11:59544205-59544206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:59537545..59539274-chr11:59543031..59545057,2	K562	blood:
2	chr11:59521605..59525070-chr11:59543036..59549785,6	MCF-7	breast:
3	chr11:59520565..59526888-chr11:59540206..59546311,15	MCF-7	breast:
4	chr11:59541502..59544247-chr11:59567174..59569666,2	MCF-7	breast:
5	chr11:59541540..59544467-chr11:59549090..59551972,2	MCF-7	breast:
6	chr11:59525592..59530085-chr11:59541874..59544413,4	MCF-7	breast:
7	chr11:59536792..59538546-chr11:59543250..59544969,2	K562	blood:
8	chr11:59543737..59545561-chr11:59553560..59556488,3	MCF-7	breast:
9	chr11:59533196..59536602-chr11:59539532..59544445,5	MCF-7	breast:
10	chr11:59544185..59546804-chr11:59574594..59577014,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166900	Chromatin interaction
ENSG00000234964	Chromatin interaction
ENSG00000254477	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10501380	1.00[CHB][hapmap]
rs11230020	1.00[CHB][hapmap]
rs11230037	1.00[CHB][hapmap]
rs1151063	1.00[CHB][hapmap]
rs1151064	1.00[CHB][hapmap]
rs11821465	1.00[CHB][hapmap]
rs12275314	1.00[EUR][1000 genomes]
rs12280446	1.00[EUR][1000 genomes]
rs12280606	1.00[CHB][hapmap]
rs12282618	1.00[EUR][1000 genomes]
rs12292682	1.00[CHB][hapmap]
rs1287111	1.00[CHB][hapmap]
rs1290460	1.00[EUR][1000 genomes]
rs17153962	1.00[JPT][hapmap]
rs17153982	1.00[JPT][hapmap]
rs17154025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17154134	1.00[CHB][hapmap]
rs17154146	1.00[CHB][hapmap]
rs17154165	1.00[CHB][hapmap]
rs17154180	1.00[CHB][hapmap]
rs17154200	1.00[CHB][hapmap]
rs17154203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17154205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154220	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154227	1.00[CHB][hapmap]
rs17596862	1.00[CHB][hapmap]
rs17597065	1.00[CHB][hapmap]
rs1938690	1.00[CHB][hapmap]
rs2298589	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447309	1.00[EUR][1000 genomes]
rs2508335	1.00[CHB][hapmap]
rs2508339	1.00[EUR][1000 genomes]
rs2509274	1.00[CHB][hapmap]
rs2509275	1.00[CHB][hapmap]
rs2509279	1.00[CHB][hapmap]
rs2509290	1.00[CHB][hapmap]
rs2509730	1.00[CHB][hapmap]
rs2927184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2957227	1.00[EUR][1000 genomes]
rs3110321	1.00[EUR][1000 genomes]
rs35211634	1.00[CHB][hapmap]
rs3781792	1.00[CHB][hapmap]
rs41340150	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41384548	1.00[CHB][hapmap]
rs4356243	1.00[CHB][hapmap]
rs4393334	1.00[CHB][hapmap]
rs472177	1.00[CHB][hapmap]
rs473679	1.00[EUR][1000 genomes]
rs473912	1.00[EUR][1000 genomes]
rs473979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs475145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs478167	1.00[CHB][hapmap]
rs478924	1.00[EUR][1000 genomes]
rs482355	1.00[CHB][hapmap]
rs482356	1.00[CHB][hapmap]
rs485803	1.00[CHB][hapmap]
rs486952	1.00[JPT][hapmap]
rs493025	1.00[EUR][1000 genomes]
rs498099	1.00[CHB][hapmap]
rs498165	1.00[EUR][1000 genomes]
rs501288	1.00[EUR][1000 genomes]
rs504016	1.00[CHB][hapmap]
rs504320	1.00[EUR][1000 genomes]
rs506384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs508411	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs511263	1.00[EUR][1000 genomes]
rs512194	1.00[CHB][hapmap]
rs512690	1.00[EUR][1000 genomes]
rs513979	1.00[CHB][hapmap]
rs516912	1.00[CHB][hapmap]
rs519605	1.00[CHB][hapmap]
rs520622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs523016	1.00[CHB][hapmap]
rs524102	1.00[CHB][hapmap]
rs528525	1.00[CHB][hapmap]
rs529270	1.00[CHB][hapmap]
rs532293	1.00[EUR][1000 genomes]
rs533166	1.00[CHB][hapmap]
rs536544	1.00[CHB][hapmap]
rs537595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs540684	1.00[CHB][hapmap]
rs549086	1.00[CHB][hapmap]
rs550449	1.00[EUR][1000 genomes]
rs552601	1.00[CHB][hapmap]
rs554460	1.00[EUR][1000 genomes]
rs554848	1.00[CHB][hapmap]
rs555251	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs558569	1.00[EUR][1000 genomes]
rs559150	1.00[JPT][hapmap]
rs559192	1.00[EUR][1000 genomes]
rs565026	1.00[EUR][1000 genomes]
rs565482	1.00[JPT][hapmap]
rs567253	1.00[EUR][1000 genomes]
rs571451	1.00[EUR][1000 genomes]
rs572138	1.00[EUR][1000 genomes]
rs573592	1.00[CHB][hapmap]
rs577224	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs577644	1.00[EUR][1000 genomes]
rs579373	1.00[CHB][hapmap]
rs59057725	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60146927	1.00[EUR][1000 genomes]
rs60628632	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60659006	1.00[EUR][1000 genomes]
rs61370741	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61463035	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7114773	0.89[YRI][hapmap]
rs7119778	1.00[CHB][hapmap]
rs7123969	1.00[CHB][hapmap]
rs7126593	1.00[CHB][hapmap]
rs7131059	1.00[CHB][hapmap]
rs73488820	1.00[EUR][1000 genomes]
rs7937245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947036	1.00[CHB][hapmap]
rs7947514	1.00[CHB][hapmap]
rs7952024	1.00[CHB][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	nsv1046086	chr11:59520424-59561455	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59524200-59545200	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:59524400-59545600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:59524400-59557000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:59524600-59557400	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:59524600-59573800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:59524800-59553400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:59524800-59555400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:59525400-59551200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:59525600-59557800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:59530800-59545000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:59533000-59545000	Weak transcription	Brain Substantia Nigra	brain
12	chr11:59534400-59559600	Weak transcription	Fetal Brain Female	brain
13	chr11:59534600-59544600	Weak transcription	Aorta	Aorta
14	chr11:59534600-59554200	Weak transcription	HSMMtube	muscle
15	chr11:59534600-59571600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:59535200-59544800	Weak transcription	Colonic Mucosa	Colon
17	chr11:59535800-59545800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:59537600-59570400	Weak transcription	Fetal Kidney	kidney
19	chr11:59537800-59553200	Weak transcription	NHDF-Ad	bronchial
20	chr11:59538000-59545400	Genic enhancers	Fetal Intestine Large	intestine
21	chr11:59539000-59545200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:59539200-59545600	Weak transcription	Brain Anterior Caudate	brain
23	chr11:59539400-59546600	Weak transcription	Esophagus	oesophagus
24	chr11:59539600-59545000	Weak transcription	Brain Angular Gyrus	brain
25	chr11:59539600-59554200	Weak transcription	Right Ventricle	heart
26	chr11:59539800-59553000	Weak transcription	Spleen	Spleen
27	chr11:59539800-59554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:59540200-59544400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr11:59540600-59545600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:59540600-59546200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:59540800-59545000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:59540800-59550400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:59540800-59556200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr11:59540800-59559600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:59541000-59544400	Weak transcription	K562	blood
36	chr11:59541000-59560000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:59541000-59573600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:59541400-59553000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:59541600-59546200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
40	chr11:59541600-59551800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:59541800-59545600	Weak transcription	Primary T cells from cord blood	blood
42	chr11:59541800-59548200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:59541800-59559200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:59542200-59546200	Strong transcription	Ovary	ovary
45	chr11:59542200-59571400	Weak transcription	Thymus	Thymus
46	chr11:59542400-59547600	Genic enhancers	Fetal Intestine Small	intestine
47	chr11:59542600-59554200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr11:59542800-59545000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:59542800-59545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:59542800-59545800	Genic enhancers	Rectal Mucosa Donor 31	rectum

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