Variant report

Variant	rs494003
Chromosome Location	chr11:65542298-65542299
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65478329..65480745-chr11:65539955..65542760,2	K562	blood:
2	chr11:65541575..65543140-chr11:65661807..65663676,2	K562	blood:
3	chr11:65541196..65542302-chr11:65585324..65586423,16	MCF-7	breast:
4	chr11:65526354..65531692-chr11:65541770..65544711,4	K562	blood:
5	chr11:65541440..65543301-chr11:65615603..65618141,2	MCF-7	breast:
6	chr11:65540229..65542418-chr11:65625485..65628418,2	K562	blood:
7	chr11:65541153..65542313-chr11:65585085..65586334,9	MCF-7	breast:
8	chr11:65477516..65483320-chr11:65539054..65543224,6	MCF-7	breast:
9	chr11:65542097..65543691-chr11:65617255..65620134,2	MCF-7	breast:
10	chr11:65541717..65544570-chr11:65625545..65627140,2	MCF-7	breast:
11	chr11:65541294..65543151-chr11:65564058..65566892,2	K562	blood:
12	chr11:65541377..65543280-chr11:65554210..65556466,3	K562	blood:
13	chr11:65509847..65512521-chr11:65541079..65543934,2	K562	blood:
14	chr11:65478022..65480745-chr11:65539955..65542379,2	K562	blood:
15	chr11:65494883..65497549-chr11:65540068..65542666,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172977	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000255404	Chromatin interaction
ENSG00000172818	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896043	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227261	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11227283	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11227284	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227288	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227303	0.90[EUR][1000 genomes]
rs1151488	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs1193851	0.85[CHB][hapmap]
rs1205259	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs12273982	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12287832	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1784223	0.85[CHB][hapmap]
rs1787034	0.85[CHB][hapmap];0.94[CHD][hapmap]
rs3372	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs4930304	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs578056	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7122657	0.85[CHB][hapmap]
rs7944860	0.85[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs494003	SNX32	cis	cerebellum	SCAN
rs494003	SIPA1	cis	cerebellum	SCAN
rs494003	SNX32	cis	parietal	SCAN
rs494003	IZUMO2	trans	parietal	SCAN
rs494003	RNASEH2C	cis	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65532400-65542600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:65532600-65544000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr11:65533600-65543600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:65534200-65544600	Weak transcription	Osteobl	bone
5	chr11:65534400-65543800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:65537000-65543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:65537400-65542400	Weak transcription	Adipose Nuclei	Adipose
8	chr11:65537400-65542800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr11:65537400-65543000	Weak transcription	Primary T cells from cord blood	blood
10	chr11:65537400-65544200	Weak transcription	NHLF	lung
11	chr11:65537400-65544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:65537400-65544400	Weak transcription	Dnd41	blood
13	chr11:65537400-65544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:65537400-65544600	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:65537400-65544600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:65537400-65544800	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:65537400-65545200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:65537400-65546600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:65537400-65546600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:65537600-65542400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:65537600-65542600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:65537600-65544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:65537600-65545000	Weak transcription	Aorta	Aorta
24	chr11:65537600-65546600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:65537800-65543800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:65537800-65543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:65537800-65546800	Weak transcription	K562	blood
28	chr11:65538200-65542600	Weak transcription	HMEC	breast
29	chr11:65538800-65543800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:65538800-65544400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:65539000-65542400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:65539000-65542800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:65539000-65544200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:65539000-65544200	Weak transcription	Gastric	stomach
35	chr11:65539000-65544400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:65539400-65543800	Weak transcription	Fetal Intestine Large	intestine
37	chr11:65539600-65543800	Weak transcription	HepG2	liver
38	chr11:65539600-65546600	Weak transcription	Stomach Mucosa	stomach
39	chr11:65540200-65544800	Weak transcription	HUVEC	blood vessel
40	chr11:65540400-65543800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:65540400-65543800	Weak transcription	HSMM	muscle
42	chr11:65540600-65542400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:65540600-65542800	Weak transcription	Thymus	Thymus
44	chr11:65540600-65544200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr11:65540600-65545800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:65540800-65544200	Weak transcription	Brain Germinal Matrix	brain
47	chr11:65541000-65544200	Weak transcription	Fetal Thymus	thymus
48	chr11:65541200-65542400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:65541200-65542400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:65541200-65544400	Weak transcription	Fetal Brain Female	brain

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