Variant report

Variant	rs2234458
Chromosome Location	chr11:65639374-65639375
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65636346-65639953	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr11:65616755-65639999	U87	brain:	n/a	n/a
3	POLR2A	chr11:65639348-65639700	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr11:65616706-65640269	U87	brain:	n/a	n/a
5	POLR2A	chr11:65639171-65639940	U87	brain:	n/a	n/a
6	POLR2A	chr11:65633886-65639510	K562	blood:	n/a	n/a
7	POLR2A	chr11:65639145-65639994	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr11:65639126-65639835	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr11:65639061-65641539	IMR90	lung:	n/a	chr11:65641273-65641282
10	MAZ	chr11:65638665-65641701	IMR90	lung:	n/a	chr11:65639908-65639918 chr11:65640385-65640395 chr11:65640115-65640124
11	POLR2A	chr11:65636912-65639982	K562	blood:	n/a	n/a
12	POLR2A	chr11:65636785-65639990	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:65633979-65640025	GM12892	blood:	n/a	n/a
14	POLR2A	chr11:65634001-65639492	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr11:65638861-65641499	ProgFib	skin:	n/a	n/a
16	POLR2A	chr11:65635289-65639598	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:65633995-65639964	GM12892	blood:	n/a	n/a
18	POLR2A	chr11:65639349-65641488	HUVEC	blood vessel:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65482061..65486231-chr11:65638918..65641829,3	K562	blood:
2	chr11:65638895..65641565-chr11:65834356..65837225,2	K562	blood:
3	chr11:65477979..65480813-chr11:65636240..65639820,3	K562	blood:
4	chr11:65478490..65481819-chr11:65637441..65641209,4	K562	blood:
5	chr11:65636578..65639381-chr11:65766938..65769474,2	MCF-7	breast:
6	chr11:65638377..65641229-chr11:65727913..65730693,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CFL1-3	chr11:65638887-65639489	NONHSAT022239

No data

Variant related genes	Relation type
EFEMP2	TF binding region
ENSG00000175467	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000175376	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2303384	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303385	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625652	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7102454	0.84[EUR][1000 genomes]
rs7940691	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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 target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897763	chr11:65613348-65644027	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	121 gene(s)	inside rSNPs	diseases
10	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
11	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
12	nsv897766	chr11:65624025-65644027	Transcr. at gene 5' and 3' Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
13	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
14	esv999644	chr11:65636167-65646034	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	esv1797198	chr11:65637273-65642343	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2234458	CTSW	Cis_1M	lymphoblastoid	RTeQTL
rs2234458	CTSW	cis	lung	GTEx
rs2234458	SNX32	cis	Thyroid	GTEx
rs2234458	CTSW	cis	Artery Tibial	GTEx
rs2234458	CTSW	cis	Thyroid	GTEx
rs2234458	CTSW	cis	Whole Blood	GTEx
rs2234458	SNX32	cis	Artery Aorta	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65628800-65639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:65629000-65639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:65632200-65639400	Weak transcription	Fetal Kidney	kidney
4	chr11:65633000-65639400	Weak transcription	Psoas Muscle	Psoas
5	chr11:65633400-65640600	Weak transcription	Hela-S3	cervix
6	chr11:65633600-65639400	Weak transcription	Brain Angular Gyrus	brain
7	chr11:65633600-65640400	Weak transcription	HMEC	breast
8	chr11:65634400-65639600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:65634800-65639600	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:65634800-65640400	Weak transcription	Primary T cells from cord blood	blood
11	chr11:65635000-65639800	Weak transcription	Small Intestine	intestine
12	chr11:65635000-65640000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:65635200-65640400	Weak transcription	Dnd41	blood
14	chr11:65635600-65639600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:65635600-65640600	Weak transcription	K562	blood
16	chr11:65635800-65640600	Weak transcription	A549	lung
17	chr11:65636000-65639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:65636200-65639400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:65636200-65640400	Weak transcription	NHEK	skin
20	chr11:65636600-65639400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:65637000-65639800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:65637200-65639400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:65637200-65640200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:65637400-65640400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:65637600-65639600	Enhancers	Primary hematopoietic stem cells	blood
26	chr11:65637600-65639800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr11:65637600-65640400	Enhancers	Primary B cells from cord blood	blood
28	chr11:65637800-65639400	Weak transcription	Aorta	Aorta
29	chr11:65637800-65640400	Enhancers	Primary T cells fromperipheralblood	blood
30	chr11:65638000-65639400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr11:65638000-65639400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr11:65638000-65639600	Weak transcription	Gastric	stomach
33	chr11:65638000-65639600	Enhancers	GM12878-XiMat	blood
34	chr11:65638000-65640000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr11:65638000-65640400	Enhancers	Primary B cells from peripheral blood	blood
36	chr11:65638000-65640400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:65638200-65640400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:65638400-65639400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:65638400-65639400	Enhancers	Lung	lung
40	chr11:65638400-65639800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr11:65638400-65639800	Flanking Active TSS	NH-A	brain
42	chr11:65638400-65640000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:65638400-65640400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:65638600-65639400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:65638600-65639400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:65638600-65639400	Enhancers	Esophagus	oesophagus
47	chr11:65638600-65639400	Enhancers	Right Atrium	heart
48	chr11:65638600-65639400	Flanking Active TSS	HSMM	muscle
49	chr11:65638600-65639600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:65638600-65639600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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