Variant report

Variant	rs12286778
Chromosome Location	chr11:46321827-46321828
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46258381..46272821-chr11:46315090..46322037,29	K562	blood:
2	chr11:46257101..46259432-chr11:46320303..46322157,2	MCF-7	breast:
3	chr11:46255391..46271183-chr11:46315085..46324739,29	K562	blood:
4	chr11:46276687..46279221-chr11:46320617..46322346,2	K562	blood:
5	chr11:46321285..46322187-chr11:46329637..46330365,2	MCF-7	breast:
6	chr11:46319743..46322548-chr11:46366934..46370497,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254639	Chromatin interaction
ENSG00000149091	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10838595	0.95[EUR][1000 genomes]
rs11038851	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12273276	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303435	0.82[GIH][hapmap]
rs4625425	0.82[GIH][hapmap]
rs7124003	0.97[EUR][1000 genomes]
rs7127254	0.84[CEU][hapmap]
rs72910053	0.90[ASN][1000 genomes]
rs7924718	0.84[GIH][hapmap];0.82[YRI][hapmap]
rs7929630	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	nsv554201	chr11:46281835-46422686	Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv825867	chr11:46303184-46425613	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS 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	21 gene(s)	inside rSNPs	diseases
3	esv1797501	chr11:46315437-46402521	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	esv1811345	chr11:46317062-46438072	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12286778	FNBP4	cis	cerebellum	SCAN
rs12286778	API5	cis	cerebellum	SCAN
rs12286778	KRR1	trans	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46318200-46330200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:46319000-46326800	Weak transcription	Esophagus	oesophagus
3	chr11:46319000-46329200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:46319200-46323800	Weak transcription	Fetal Lung	lung
5	chr11:46319200-46323800	Weak transcription	HSMMtube	muscle
6	chr11:46319200-46324000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:46319200-46326000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:46319200-46326600	Weak transcription	Placenta	Placenta
9	chr11:46319200-46328200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:46319200-46329200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:46319200-46330000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:46319200-46330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:46319200-46330400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:46319200-46337600	Weak transcription	Right Ventricle	heart
15	chr11:46319200-46342000	Weak transcription	Ovary	ovary
16	chr11:46319400-46322800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:46319400-46330200	Weak transcription	Colonic Mucosa	Colon
18	chr11:46319400-46346000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:46319600-46322000	Genic enhancers	HSMM	muscle
20	chr11:46319600-46328200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:46319600-46328800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:46320200-46322000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:46320200-46322200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr11:46320400-46329200	Strong transcription	Fetal Stomach	stomach
25	chr11:46320600-46322200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:46320800-46324800	Strong transcription	Fetal Intestine Large	intestine
27	chr11:46321000-46324800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr11:46321000-46325000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:46321000-46325600	Strong transcription	Fetal Muscle Leg	muscle
30	chr11:46321000-46328000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:46321200-46322000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:46321200-46322400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:46321200-46323000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr11:46321200-46324800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:46321200-46326600	Strong transcription	Fetal Intestine Small	intestine
36	chr11:46321400-46322000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:46321400-46322000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:46321400-46322000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr11:46321400-46322000	Strong transcription	Gastric	stomach
40	chr11:46321400-46322000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr11:46321400-46322000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:46321400-46322000	Strong transcription	K562	blood
43	chr11:46321400-46322000	Genic enhancers	NHDF-Ad	bronchial
44	chr11:46321400-46322200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:46321400-46322200	Enhancers	GM12878-XiMat	blood
46	chr11:46321400-46322200	Genic enhancers	NHLF	lung
47	chr11:46321400-46330200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:46321400-46331400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:46321400-46340200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr11:46321600-46322000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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