Variant report

Variant	rs658524
Chromosome Location	chr11:65647260-65647261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65647201-65647387	K562	blood:	n/a	n/a
2	MAX	chr11:65647137-65647514	NB4	blood:	n/a	n/a
3	POLR2A	chr11:65647156-65647686	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr11:65647024-65647525	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:65646968-65647705	K562	blood:	n/a	n/a
6	POLR2A	chr11:65647110-65647779	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr11:65647216-65647369	A549	lung:	n/a	n/a
8	POLR2A	chr11:65647139-65647404	A549	lung:	n/a	n/a
9	POLR2A	chr11:65647111-65647442	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:65647135-65647518	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr11:65647165-65647455	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:65647092-65647732	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:65647161-65647445	ECC-1	luminal epithelium:	n/a	n/a
14	MYC	chr11:65647112-65647531	NB4	blood:	n/a	n/a
15	POLR2A	chr11:65647080-65647533	ECC-1	luminal epithelium:	n/a	n/a
16	EBF1	chr11:65647155-65647454	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:65647121-65647556	HL-60	blood:	n/a	n/a
18	POLR2A	chr11:65647159-65647749	U87	brain:	n/a	n/a
19	POLR2A	chr11:65647174-65647441	MCF-7	breast:	n/a	n/a
20	POLR2A	chr11:65647165-65647588	U87	brain:	n/a	n/a
21	POLR2A	chr11:65647138-65647409	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:65647125-65647441	A549	lung:	n/a	n/a
23	POLR2A	chr11:65647056-65647518	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:65647102-65647605	HL-60	blood:	n/a	n/a
25	POLR2A	chr11:65647162-65647538	K562	blood:	n/a	n/a
26	PML	chr11:65647169-65647539	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:65647108-65647803	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr11:65647227-65647384	Hela-S3	cervix:	n/a	n/a
29	RUNX3	chr11:65647062-65647420	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:65647183-65647410	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr11:65647082-65647656	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr11:65647108-65647610	GM12892	blood:	n/a	n/a
33	RUNX3	chr11:65647097-65647358	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:65647008-65647848	PANC-1	pancreas:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65646632..65650808-chr11:65654844..65660529,6	MCF-7	breast:

No data

Variant related genes	Relation type
CTSW	TF binding region
ENSG00000172500	Chromatin interaction
ENSG00000175602	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10791830	0.94[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151519	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204650	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225345	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2231884	1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes]
rs2303385	0.94[ASW][hapmap];0.83[CHB][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs507062	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs568617	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583887	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585557	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58568715	0.82[EUR][1000 genomes]
rs588114	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs596002	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608616	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs622614	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625652	0.86[AFR][1000 genomes]
rs641018	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656980	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs658938	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677931	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687672	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693824	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694994	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940691	0.83[CHB][hapmap];0.84[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	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

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs658524	SNX32	cis	Esophagus Mucosa	GTEx
rs658524	CTSW	cis	Nerve Tibial	GTEx
rs658524	CTSW	cis	Stomach	GTEx
rs658524	FIBP	cis	lymphoblastoid	seeQTL
rs658524	SNX32	cis	Artery Aorta	GTEx
rs658524	CTSW	cis	Esophagus Muscularis	GTEx
rs658524	SNX32	cis	Skin Sun Exposed Lower leg	GTEx
rs658524	CTSW	cis	Artery Tibial	GTEx
rs658524	FIBP	cis	multi-tissue	Pritchard
rs658524	SNX32	cis	Nerve Tibial	GTEx
rs658524	FIBP	Cis_1M	lymphoblastoid	RTeQTL
rs658524	CTSW	cis	Thyroid	GTEx
rs658524	SNX32	cis	Esophagus Muscularis	GTEx
rs658524	SNX32	cis	Thyroid	GTEx
rs658524	CTSW	Cis_1M	lymphoblastoid	RTeQTL
rs658524	CTSW	cis	Skin Sun Exposed Lower leg	GTEx
rs658524	SNX32	cis	Artery Tibial	GTEx
rs658524	CTSW	cis	Lymphoblastoid	GTEx
rs658524	CTSW	cis	lymphoblastoid	seeQTL
rs658524	CTSW	cis	Artery Aorta	GTEx
rs658524	CTSW	cis	multi-tissue	Pritchard
rs658524	CTSW	cis	lung	GTEx
rs658524	CTSW	cis	Whole Blood	GTEx
rs658524	CTSW	cis	Esophagus Mucosa	GTEx
rs658524	FIBP	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65641000-65654400	Weak transcription	Fetal Heart	heart
2	chr11:65641400-65648600	Weak transcription	Spleen	Spleen
3	chr11:65641400-65648600	Weak transcription	HUVEC	blood vessel
4	chr11:65641400-65648800	Weak transcription	HSMMtube	muscle
5	chr11:65641400-65649000	Weak transcription	Right Ventricle	heart
6	chr11:65641400-65649200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:65641400-65649200	Weak transcription	Lung	lung
8	chr11:65641400-65649400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:65641400-65649600	Weak transcription	Gastric	stomach
10	chr11:65641400-65649800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:65641400-65649800	Weak transcription	Osteobl	bone
12	chr11:65641400-65650000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:65641400-65650000	Weak transcription	Aorta	Aorta
14	chr11:65641400-65650000	Weak transcription	A549	lung
15	chr11:65641400-65650400	Weak transcription	Fetal Kidney	kidney
16	chr11:65641400-65650400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:65641400-65650600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:65641400-65651000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:65641400-65654000	Weak transcription	Small Intestine	intestine
20	chr11:65641600-65647400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:65641600-65648200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:65641600-65648200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:65641600-65648600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:65641600-65648600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:65641600-65648600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:65641600-65648800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:65641600-65648800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:65641600-65648800	Weak transcription	Brain Germinal Matrix	brain
29	chr11:65641600-65648800	Weak transcription	Fetal Brain Female	brain
30	chr11:65641600-65648800	Weak transcription	NHEK	skin
31	chr11:65641600-65648800	Weak transcription	NHLF	lung
32	chr11:65641600-65649000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:65641600-65649000	Weak transcription	Placenta	Placenta
34	chr11:65641600-65649200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:65641600-65649200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:65641600-65649200	Weak transcription	Brain Anterior Caudate	brain
37	chr11:65641600-65649400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:65641600-65649400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr11:65641600-65649600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:65641600-65649600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:65641600-65649600	Weak transcription	Brain Angular Gyrus	brain
42	chr11:65641600-65649600	Weak transcription	Brain Substantia Nigra	brain
43	chr11:65641600-65649800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:65641600-65649800	Weak transcription	Adipose Nuclei	Adipose
45	chr11:65641600-65649800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr11:65641600-65649800	Weak transcription	Ovary	ovary
47	chr11:65641600-65649800	Weak transcription	Pancreas	Pancrea
48	chr11:65641600-65650000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:65641600-65650000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:65641600-65650000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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