Variant report

Variant	rs11481
Chromosome Location	chr11:67820335-67820336
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:67815563..67818643-chr11:67818782..67821542,3	MCF-7	breast:
2	chr11:67819215..67821345-chr11:67829037..67831541,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCIRG1-1	chr11:67820290-67820552	ENSG00000255031.1
2	lnc-TCIRG1-1	chr11:67819100-67821228	NONHSAT022500

Variant related genes	Relation type
ENSG00000110719	Chromatin interaction
ENSG00000110721	Chromatin interaction
ENSG00000255031	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11228127	0.83[ASN][1000 genomes]
rs2075609	0.82[ASN][1000 genomes]
rs4147782	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036101	chr11:67346813-67828351	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv541079	chr11:67346813-67828351	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
3	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	esv2757450	chr11:67472905-67891289	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
5	esv2759835	chr11:67472905-67891289	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
6	esv2758275	chr11:67524937-67859490	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv469856	chr11:67639037-67859490	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
8	nsv482760	chr11:67639037-67859490	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
9	nsv897837	chr11:67757350-67821036	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
10	nsv897838	chr11:67757350-67833543	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
11	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
12	nsv1050471	chr11:67764068-67821610	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
13	nsv469964	chr11:67765056-67821036	Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
14	nsv897842	chr11:67765056-67821036	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
15	nsv897843	chr11:67765056-67833543	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
16	nsv897845	chr11:67774231-67821036	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
17	nsv897849	chr11:67789837-67821036	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
18	nsv897851	chr11:67793448-67821036	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
19	nsv897852	chr11:67795066-67833543	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
20	nsv555281	chr11:67796691-67821036	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
21	nsv897855	chr11:67805563-67842369	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
22	nsv897856	chr11:67806703-67821036	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11481	CHKA	cis	thalamus	BrainEAC
rs11481	CHKA	cis	occipital cortex	BrainEAC
rs11481	CHKA	cis	substantia nigra	BrainEAC
rs11481	CHKA	cis	cerebellar cortex	BrainEAC
rs11481	CHKA	cis	frontal cortex	BrainEAC
rs11481	CHKA	cis	inferior olivary nucleus	BrainEAC
rs11481	CHKA	cis	putamen	BrainEAC
rs11481	CHKA	cis	temporal cortex	BrainEAC
rs11481	CHKA	cis	hippocampus	BrainEAC
rs11481	CHKA	cis	brain	BrainEAC
rs11481	CHKA	cis	intralobular white matter	BrainEAC

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67808200-67824600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr11:67808400-67841000	Weak transcription	HMEC	breast
3	chr11:67808600-67820600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:67808600-67823600	Weak transcription	Hela-S3	cervix
5	chr11:67808600-67828200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:67808600-67832200	Weak transcription	Right Atrium	heart
7	chr11:67808800-67842600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:67809000-67821600	Strong transcription	NHLF	lung
9	chr11:67809000-67826600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:67809200-67821400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:67809200-67822600	Strong transcription	Liver	Liver
12	chr11:67809400-67821000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:67809400-67821000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:67809400-67821800	Strong transcription	Thymus	Thymus
15	chr11:67809400-67822000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:67809400-67834800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:67809600-67821000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:67809600-67821400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:67809600-67821400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:67809600-67822400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr11:67809800-67820400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:67809800-67820600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:67809800-67821800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:67809800-67822000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:67810000-67820600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:67810000-67820600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:67810200-67821400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:67810400-67820800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:67810600-67821400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:67810600-67821400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:67810600-67821600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:67810800-67821400	Strong transcription	Primary T cells from cord blood	blood
33	chr11:67810800-67828200	Weak transcription	Primary B cells from cord blood	blood
34	chr11:67811000-67821400	Strong transcription	Adipose Nuclei	Adipose
35	chr11:67811000-67822800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr11:67811000-67823000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:67811200-67821200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:67811200-67822600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr11:67811200-67841600	Strong transcription	Fetal Intestine Small	intestine
40	chr11:67811400-67820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:67811400-67821600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:67811800-67820600	Strong transcription	GM12878-XiMat	blood
43	chr11:67811800-67821200	Strong transcription	Osteobl	bone
44	chr11:67811800-67821600	Strong transcription	Fetal Thymus	thymus
45	chr11:67811800-67822400	Strong transcription	A549	lung
46	chr11:67811800-67823000	Strong transcription	Colonic Mucosa	Colon
47	chr11:67811800-67824000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:67811800-67824400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:67812000-67820800	Strong transcription	Esophagus	oesophagus
50	chr11:67812200-67823600	Strong transcription	Fetal Stomach	stomach

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