Variant report

Variant	rs12284352
Chromosome Location	chr11:107276922-107276923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11823829	0.81[EUR][1000 genomes]
rs12271885	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12274982	0.81[EUR][1000 genomes]
rs12281043	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12288600	0.82[CEU][hapmap]
rs12786041	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12807553	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4753805	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4754214	0.80[EUR][1000 genomes]
rs4754216	0.83[EUR][1000 genomes]
rs61906057	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61906058	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61908160	0.81[AFR][1000 genomes]
rs623599	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7124763	0.86[EUR][1000 genomes]
rs7125898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130701	0.81[EUR][1000 genomes]
rs7937821	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7938787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs976707	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs9787772	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9804545	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv832261	chr11:107145901-107321562	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2756363	chr11:107189790-107376790	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12284352	CWF19L2	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107195000-107299200	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:107241600-107327800	Weak transcription	HSMMtube	muscle
3	chr11:107252600-107281200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:107252600-107323800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:107255000-107327600	Weak transcription	Fetal Heart	heart
6	chr11:107256600-107298000	Weak transcription	Brain Substantia Nigra	brain
7	chr11:107256600-107327600	Weak transcription	NHDF-Ad	bronchial
8	chr11:107258600-107281600	Weak transcription	Fetal Brain Male	brain
9	chr11:107258800-107277000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr11:107258800-107291800	Weak transcription	Colonic Mucosa	Colon
11	chr11:107258800-107324200	Weak transcription	Small Intestine	intestine
12	chr11:107259000-107280400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:107259200-107299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:107259600-107323400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:107261600-107310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:107262200-107324000	Weak transcription	Pancreas	Pancrea
17	chr11:107262600-107285400	Weak transcription	Fetal Thymus	thymus
18	chr11:107262800-107283600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:107262800-107284000	Weak transcription	Fetal Kidney	kidney
20	chr11:107263200-107286000	Weak transcription	Placenta	Placenta
21	chr11:107263200-107309400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:107263200-107310200	Weak transcription	Psoas Muscle	Psoas
23	chr11:107263200-107310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:107263400-107279400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:107263400-107287000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr11:107263400-107287000	Weak transcription	HSMM	muscle
27	chr11:107263400-107298800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:107263600-107280000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:107263600-107280600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:107263600-107283800	Weak transcription	Ovary	ovary
31	chr11:107263600-107298200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:107263600-107308200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:107263600-107309400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:107263600-107309400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:107263600-107310600	Weak transcription	Brain Angular Gyrus	brain
36	chr11:107263800-107277800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr11:107268600-107299400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:107268600-107312200	Weak transcription	K562	blood
39	chr11:107268600-107323400	Weak transcription	Gastric	stomach
40	chr11:107268800-107283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:107268800-107284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:107268800-107309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:107268800-107309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:107269000-107298400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:107269000-107324600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:107269200-107288800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:107269800-107278600	Weak transcription	Fetal Intestine Large	intestine
48	chr11:107269800-107299600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:107270000-107277800	Weak transcription	HepG2	liver
50	chr11:107270000-107279000	Weak transcription	Duodenum Mucosa	Duodenum

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