Variant report

Variant	rs688241
Chromosome Location	chr11:63885769-63885770
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63884385..63886576-chr11:63893083..63896548,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRPT1-2	chr11:63885744-63886249	ENSG00000256341.1

Variant related genes	Relation type
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11549691	0.81[EUR][1000 genomes]
rs1544538	0.85[EUR][1000 genomes]
rs17851033	0.85[EUR][1000 genomes]
rs1938817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070232	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154984	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2186571	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245837	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622422	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2622424	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701530	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701536	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701539	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4980506	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs583799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59250939	0.85[EUR][1000 genomes]
rs599549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639406	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
4	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS 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	234 gene(s)	inside rSNPs	diseases
7	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
10	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
11	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
12	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
13	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs688241	HSPC152	Cis_1M	lymphoblastoid	RTeQTL
rs688241	PRDX5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63866400-63887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:63873400-63886800	Weak transcription	Colonic Mucosa	Colon
3	chr11:63875400-63896200	Weak transcription	Spleen	Spleen
4	chr11:63875600-63886800	Weak transcription	HSMMtube	muscle
5	chr11:63879200-63888400	Weak transcription	Left Ventricle	heart
6	chr11:63879600-63885800	Weak transcription	HepG2	liver
7	chr11:63879600-63886200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:63879600-63890200	Weak transcription	Liver	Liver
9	chr11:63879800-63891600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:63881200-63888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:63881800-63891800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:63882200-63889400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:63882200-63889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:63882200-63889600	Weak transcription	Lung	lung
15	chr11:63882200-63892800	Weak transcription	Fetal Kidney	kidney
16	chr11:63882800-63888000	Strong transcription	Fetal Stomach	stomach
17	chr11:63883000-63890800	Weak transcription	Dnd41	blood
18	chr11:63883200-63888400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:63883400-63885800	Strong transcription	Brain Hippocampus Middle	brain
20	chr11:63883400-63886400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:63883600-63885800	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:63883600-63886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:63883600-63888200	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:63883600-63888200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:63883800-63886000	Strong transcription	Brain Germinal Matrix	brain
26	chr11:63883800-63886000	Weak transcription	Fetal Brain Male	brain
27	chr11:63883800-63886600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr11:63883800-63888400	Weak transcription	Fetal Heart	heart
29	chr11:63884200-63885800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:63884400-63885800	Genic enhancers	Right Ventricle	heart
31	chr11:63884600-63885800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:63884600-63887200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:63884600-63889800	Weak transcription	Pancreas	Pancrea
34	chr11:63884800-63885800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:63884800-63888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:63885000-63887400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:63885000-63896600	Weak transcription	Hela-S3	cervix
38	chr11:63885200-63885800	Genic enhancers	Brain Anterior Caudate	brain
39	chr11:63885200-63888200	Weak transcription	Esophagus	oesophagus
40	chr11:63885400-63887800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:63885400-63888200	Weak transcription	Brain Angular Gyrus	brain
42	chr11:63885400-63888200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:63885400-63888400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:63885400-63889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:63885400-63892400	Weak transcription	Fetal Intestine Small	intestine
46	chr11:63885400-63898600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:63885600-63885800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:63885600-63886400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:63885600-63887800	Enhancers	Fetal Brain Female	brain
50	chr11:63885600-63888000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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