Variant report

Variant	rs489574
Chromosome Location	chr11:65542739-65542740
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65463670..65466251-chr11:65542574..65544907,2	K562	blood:
2	chr11:65478329..65480745-chr11:65539955..65542760,2	K562	blood:
3	chr11:65541575..65543140-chr11:65661807..65663676,2	K562	blood:
4	chr11:65526354..65531692-chr11:65541770..65544711,4	K562	blood:
5	chr11:65541440..65543301-chr11:65615603..65618141,2	MCF-7	breast:
6	chr11:65542483..65544503-chr11:65618278..65620229,2	K562	blood:
7	chr11:65477516..65483320-chr11:65539054..65543224,6	MCF-7	breast:
8	chr11:65542097..65543691-chr11:65617255..65620134,2	MCF-7	breast:
9	chr11:65541717..65544570-chr11:65625545..65627140,2	MCF-7	breast:
10	chr11:65541294..65543151-chr11:65564058..65566892,2	K562	blood:
11	chr11:65541377..65543280-chr11:65554210..65556466,3	K562	blood:
12	chr11:65509847..65512521-chr11:65541079..65543934,2	K562	blood:

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11227287	0.80[ASN][1000 genomes]
rs11227301	0.88[ASN][1000 genomes]
rs12361032	0.81[ASN][1000 genomes]
rs12362011	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12801669	0.87[ASN][1000 genomes]
rs1308020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34946581	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35696016	0.88[ASN][1000 genomes]
rs35727622	0.83[ASN][1000 genomes]
rs3759034	0.87[ASN][1000 genomes]
rs565427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61895678	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs620088	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs489574	RNASEH2C	cis	parietal	SCAN
rs489574	C11orf48	cis	cerebellum	SCAN
rs489574	DKFZp761E198	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65532600-65544000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr11:65533600-65543600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:65534200-65544600	Weak transcription	Osteobl	bone
4	chr11:65534400-65543800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:65537000-65543800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:65537400-65542800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr11:65537400-65543000	Weak transcription	Primary T cells from cord blood	blood
8	chr11:65537400-65544200	Weak transcription	NHLF	lung
9	chr11:65537400-65544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:65537400-65544400	Weak transcription	Dnd41	blood
11	chr11:65537400-65544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:65537400-65544600	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:65537400-65544600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:65537400-65544800	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:65537400-65545200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:65537400-65546600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:65537400-65546600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:65537600-65544200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:65537600-65545000	Weak transcription	Aorta	Aorta
20	chr11:65537600-65546600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:65537800-65543800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:65537800-65543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:65537800-65546800	Weak transcription	K562	blood
24	chr11:65538800-65543800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:65538800-65544400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:65539000-65542800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:65539000-65544200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:65539000-65544200	Weak transcription	Gastric	stomach
29	chr11:65539000-65544400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:65539400-65543800	Weak transcription	Fetal Intestine Large	intestine
31	chr11:65539600-65543800	Weak transcription	HepG2	liver
32	chr11:65539600-65546600	Weak transcription	Stomach Mucosa	stomach
33	chr11:65540200-65544800	Weak transcription	HUVEC	blood vessel
34	chr11:65540400-65543800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:65540400-65543800	Weak transcription	HSMM	muscle
36	chr11:65540600-65542800	Weak transcription	Thymus	Thymus
37	chr11:65540600-65544200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr11:65540600-65545800	Weak transcription	Brain Substantia Nigra	brain
39	chr11:65540800-65544200	Weak transcription	Brain Germinal Matrix	brain
40	chr11:65541000-65544200	Weak transcription	Fetal Thymus	thymus
41	chr11:65541200-65544400	Weak transcription	Fetal Brain Female	brain
42	chr11:65541200-65544600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:65541400-65544600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr11:65541600-65543600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:65541600-65543800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:65541600-65544200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:65541800-65543800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:65541800-65544000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:65541800-65544800	Enhancers	Pancreas	Pancrea
50	chr11:65542000-65543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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