Variant report

Variant	rs11662523
Chromosome Location	chr18:12357290-12357291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12309708..12311780-chr18:12356132..12358886,2	K562	blood:
2	chr18:12356851..12359830-chr18:12373895..12378079,5	K562	blood:
3	chr18:12356081..12357998-chr18:12375815..12378034,2	K562	blood:
4	chr18:12357213..12360142-chr18:12658246..12659878,2	K562	blood:
5	chr18:12357078..12360021-chr18:12368402..12370925,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141385	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10459999	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10460000	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10460001	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10853225	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11080564	0.95[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs11080565	0.85[AMR][1000 genomes]
rs11080569	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11080571	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11080572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129115	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11553521	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11664216	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11665134	0.82[AMR][1000 genomes]
rs11875938	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12455273	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12456857	0.95[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs12604732	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12954686	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12968089	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12968566	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1547858	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1941222	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003881	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298542	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298543	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2509510	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28372882	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34829762	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35968035	0.83[ASN][1000 genomes]
rs3786260	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs478088	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4796961	0.85[AMR][1000 genomes]
rs4797677	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797680	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs553091	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs566960	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs693449	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7231182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7231409	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235237	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7235296	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7407640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7504908	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7504974	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7505834	0.95[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs8086821	0.85[AMR][1000 genomes]
rs8086993	0.82[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs8087840	0.82[AMR][1000 genomes]
rs8092506	0.95[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8093375	0.81[CEU][hapmap]
rs8097342	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303769	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303770	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs9303771	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9635829	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9956171	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9960103	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9964406	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11662523	MEST	trans	lymphoblastoid	seeQTL
rs11662523	TUBB6	cis	Whole Blood	GTEx
rs11662523	TUBB6	cis	multi-tissue	Pritchard
rs11662523	TUBB6	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12333200-12362200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
7	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
8	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
9	chr18:12333600-12358200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr18:12333600-12361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr18:12333600-12362600	Strong transcription	Adipose Nuclei	Adipose
12	chr18:12333600-12364000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr18:12333600-12366400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
15	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr18:12333800-12360200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr18:12335600-12362600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr18:12337000-12367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr18:12337200-12359800	Strong transcription	Fetal Intestine Large	intestine
23	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:12337400-12369800	Strong transcription	Liver	Liver
25	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr18:12337800-12360200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr18:12337800-12360600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:12338600-12359600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr18:12339200-12368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr18:12339800-12359600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr18:12339800-12362000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr18:12339800-12371400	Strong transcription	Dnd41	blood
36	chr18:12340000-12361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:12340000-12362000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr18:12340000-12365000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr18:12340000-12369400	Strong transcription	HepG2	liver
41	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr18:12340000-12371400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:12340000-12371600	Strong transcription	GM12878-XiMat	blood
45	chr18:12340200-12361600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr18:12340200-12366400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr18:12340200-12369400	Strong transcription	Hela-S3	cervix
48	chr18:12340400-12359800	Strong transcription	Osteobl	bone
49	chr18:12340400-12367400	Strong transcription	Thymus	Thymus
50	chr18:12340800-12360000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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