Variant report

Variant	rs2303385
Chromosome Location	chr11:65640562-65640563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65640325-65641585	U87	brain:	n/a	n/a
2	STAT5A	chr11:65640480-65641110	GM12878	blood:	n/a	n/a
3	JUN	chr11:65640385-65641486	K562	blood:	n/a	n/a
4	POLR2A	chr11:65640261-65641434	K562	blood:	n/a	n/a
5	SREBP2	chr11:65640337-65641826	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:65640023-65641431	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr11:65639380-65641544	SK-N-SH	brain:	n/a	chr11:65641273-65641282
8	HCFC1	chr11:65640375-65641466	Hela-S3	cervix:	n/a	n/a
9	MTA3	chr11:65640445-65641603	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:65640363-65641475	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:65640092-65641466	U87	brain:	n/a	n/a
12	POLR2A	chr11:65640424-65641502	H1-neurons	neurons:	n/a	n/a
13	CTCF	chr11:65640520-65640670	AG09319	gingival:	n/a	n/a
14	POLR2A	chr11:65639629-65641407	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:65640497-65641490	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr11:65640429-65641603	GM12878	blood:	n/a	n/a
17	ZBTB7A	chr11:65640058-65641488	ECC-1	luminal epithelium:	n/a	chr11:65640518-65640526 chr11:65640517-65640525
18	POLR2A	chr11:65640317-65641520	H1-neurons	neurons:	n/a	n/a
19	ZBTB7A	chr11:65640217-65641427	K562	blood:	n/a	chr11:65640518-65640526 chr11:65640517-65640525
20	POLR2A	chr11:65640538-65641429	K562	blood:	n/a	n/a
21	MXI1	chr11:65639061-65641539	IMR90	lung:	n/a	chr11:65641273-65641282
22	POLR2A	chr11:65640325-65641450	U87	brain:	n/a	n/a
23	MAZ	chr11:65638665-65641701	IMR90	lung:	n/a	chr11:65639908-65639918 chr11:65640385-65640395 chr11:65640115-65640124
24	POLR2A	chr11:65640268-65641466	U87	brain:	n/a	n/a
25	POLR2A	chr11:65640556-65640591	HepG2	liver:	n/a	n/a
26	POLR2A	chr11:65638861-65641499	ProgFib	skin:	n/a	n/a
27	NR2F2	chr11:65640474-65641540	K562	blood:	n/a	n/a
28	PML	chr11:65640503-65641517	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:65640554-65641580	K562	blood:	n/a	n/a
30	ZBTB7A	chr11:65640035-65641482	ECC-1	luminal epithelium:	n/a	chr11:65640518-65640526 chr11:65640517-65640525
31	POLR2A	chr11:65640286-65641464	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr11:65639349-65641488	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:65640516-65640566	Hela-S3	cervix:	n/a
2	chr11:65640516-65640566	RPTEC	kidney:	n/a
3	chr11:65640516-65640566	MCF-7	breast:	n/a
4	chr11:65640516-65640566	A549	lung:	n/a
5	chr11:65640516-65640566	Hepatocyte	liver:	n/a
6	chr11:65640516-65640566	AG04450	lung:	fetal
7	chr11:65640516-65640566	AG09319	gingival:	n/a
8	chr11:65640516-65640566	NT2-D1	testis:	n/a
9	chr11:65640516-65640566	HEEpiC	esophagus:	n/a
10	chr11:65640516-65640566	SK-N-SH_RA	brain:	n/a
11	chr11:65640516-65640566	LNCaP	prostate:	n/a
12	chr11:65640516-65640566	NB4	blood:	n/a
13	chr11:65640516-65640566	HCT-116	colon:	n/a
14	chr11:65640516-65640566	AoSMC	blood vessel:	n/a
15	chr11:65640516-65640566	NH-A	brain:	n/a
16	chr11:65640516-65640566	HRCEpiC	kidney:	n/a
17	chr11:65640516-65640566	HRPEpiC	eye:	n/a
18	chr11:65640516-65640566	HCPEpiC	choroid plexus:	n/a
19	chr11:65640516-65640566	K562	blood:	n/a
20	chr11:65640516-65640566	BE2_C	brain:	n/a
21	chr11:65640516-65640566	SK-N-SH	brain:	n/a
22	chr11:65640516-65640566	AG04449	skin:	fetal
23	chr11:65640516-65640566	HCF	heart:	n/a
24	chr11:65640516-65640566	AG09309	skin:	n/a
25	chr11:65640516-65640566	GM19239	blood:	n/a
26	chr11:65640516-65640566	HMEC	breast:	n/a
27	chr11:65640516-65640566	GM12891	blood:	n/a
28	chr11:65640516-65640566	GM06990	blood:	n/a
29	chr11:65640516-65640566	GM12892	blood:	n/a
30	chr11:65640516-65640566	ovcar-3	ovarian:	n/a
31	chr11:65640516-65640566	Caco-2	colon:	n/a
32	chr11:65640516-65640566	NHBE	bronchial:	n/a
33	chr11:65640516-65640566	HUVEC	blood vessel:	n/a
34	chr11:65640516-65640566	U87	brain:	n/a
35	chr11:65640516-65640566	HNPCEpiC	eye:	n/a
36	chr11:65640516-65640566	HepG2	liver:	n/a
37	chr11:65640516-65640566	HRE	kidney:	n/a
38	chr11:65640516-65640566	ProgFib	skin:	n/a
39	chr11:65640516-65640566	SK-N-MC	brain:	n/a
40	chr11:65640516-65640566	MCF10A-Er-Src	breast:	n/a
41	chr11:65640516-65640566	NHDF-neo	bronchial:	n/a
42	chr11:65640516-65640566	HAEpiC	amniotic membrane:	n/a
43	chr11:65640516-65640566	SKMC	muscle:	n/a
44	chr11:65640516-65640566	Jurkat	blood:	n/a
45	chr11:65640516-65640566	ECC-1	luminal epithelium:	n/a
46	chr11:65640516-65640566	BJ	skin:	n/a
47	chr11:65640516-65640566	AG10803	skin:	n/a
48	chr11:65640516-65640566	SAEC	small airway:	n/a
49	chr11:65640516-65640566	PrEC	prostate:	n/a
50	chr11:65640516-65640566	CMK	blood:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65640551..65642134-chr11:65685115..65687811,2	MCF-7	breast:
2	chr11:65482061..65486231-chr11:65638918..65641829,3	K562	blood:
3	chr11:65638895..65641565-chr11:65834356..65837225,2	K562	blood:
4	chr11:65547235..65549033-chr11:65639667..65642031,2	K562	blood:
5	chr11:65639484..65641571-chr8:144697740..144699528,2	MCF-7	breast:
6	chr11:65478490..65481819-chr11:65637441..65641209,4	K562	blood:
7	chr11:65638377..65641229-chr11:65727913..65730693,2	MCF-7	breast:

No data

Variant related genes	Relation type
EFEMP2	TF binding region
EFEMP2	CpG island
ENSG00000175467	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000104522	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11227306	0.92[CEU][hapmap];0.91[MEX][hapmap]
rs1151519	0.82[AFR][1000 genomes]
rs1204650	0.80[AFR][1000 genomes]
rs12800497	0.92[CEU][hapmap]
rs2234458	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303384	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs568617	0.94[ASW][hapmap];0.83[CHB][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs583887	0.94[ASW][hapmap];0.83[CHB][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs596002	0.83[AFR][1000 genomes]
rs601863	0.94[ASW][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs625652	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641018	0.83[CHB][hapmap];0.86[YRI][hapmap]
rs645900	0.94[ASW][hapmap];0.83[CHB][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs656980	0.94[ASW][hapmap];0.83[CHB][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs658524	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]
rs658938	0.94[ASW][hapmap];0.83[CHB][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs687672	0.94[ASW][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs694994	0.94[ASW][hapmap];0.83[CHB][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs7102454	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7928652	0.92[CEU][hapmap]
rs7940691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
16	esv3371600	chr11:65640076-65645374	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2303385	CTSW	cis	Whole Blood	GTEx
rs2303385	EIF1AD	cis	parietal	SCAN
rs2303385	FRMD8	cis	parietal	SCAN
rs2303385	EFEMP2	cis	cerebellum	SCAN
rs2303385	CTSW	cis	Artery Tibial	GTEx
rs2303385	TPCN2	cis	cerebellum	SCAN
rs2303385	SNX32	cis	Artery Aorta	GTEx
rs2303385	CTSW	cis	lung	GTEx
rs2303385	LRRN4CL	cis	cerebellum	SCAN
rs2303385	CTSW	Cis_1M	lymphoblastoid	RTeQTL
rs2303385	CTSW	cis	Thyroid	GTEx
rs2303385	SNX32	cis	cerebellum	SCAN
rs2303385	CTSW	cis	lymphoblastoid	seeQTL
rs2303385	FIBP	cis	lymphoblastoid	seeQTL
rs2303385	SNX32	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65633400-65640600	Weak transcription	Hela-S3	cervix
2	chr11:65635600-65640600	Weak transcription	K562	blood
3	chr11:65635800-65640600	Weak transcription	A549	lung
4	chr11:65639200-65640600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:65639200-65640600	Enhancers	Fetal Brain Male	brain
6	chr11:65639200-65641600	Active TSS	Brain Substantia Nigra	brain
7	chr11:65639400-65640600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:65639400-65640600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:65639400-65640600	Active TSS	Brain Cingulate Gyrus	brain
10	chr11:65639400-65640600	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr11:65639400-65640600	Active TSS	Osteobl	bone
12	chr11:65639400-65640800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr11:65639400-65641000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr11:65639400-65641400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:65639400-65641400	Active TSS	Aorta	Aorta
16	chr11:65639400-65641400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr11:65639400-65641400	Active TSS	Fetal Kidney	kidney
18	chr11:65639400-65641600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:65639400-65641600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:65639400-65641600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:65639400-65641600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:65639400-65641600	Active TSS	Brain Angular Gyrus	brain
23	chr11:65639400-65641600	Active TSS	Right Atrium	heart
24	chr11:65639400-65641600	Active TSS	HSMM	muscle
25	chr11:65639400-65641600	Active TSS	NHDF-Ad	bronchial
26	chr11:65639600-65640600	Active TSS	NHLF	lung
27	chr11:65639600-65641000	Active TSS	Fetal Heart	heart
28	chr11:65639600-65641200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:65639600-65641200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr11:65639600-65641200	Active TSS	Brain Hippocampus Middle	brain
31	chr11:65639600-65641200	Active TSS	Esophagus	oesophagus
32	chr11:65639600-65641200	Active TSS	Fetal Stomach	stomach
33	chr11:65639600-65641200	Active TSS	Placenta Amnion	Placenta Amnion
34	chr11:65639600-65641400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:65639600-65641400	Active TSS	Gastric	stomach
36	chr11:65639600-65641600	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:65639600-65641600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr11:65639600-65641600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:65639600-65641600	Active TSS	Colon Smooth Muscle	Colon
40	chr11:65639600-65641600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr11:65639600-65641600	Active TSS	Left Ventricle	heart
42	chr11:65639600-65641600	Active TSS	Ovary	ovary
43	chr11:65639600-65641800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:65639800-65640600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:65639800-65640600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:65639800-65640600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr11:65639800-65640600	Active TSS	Fetal Lung	lung
48	chr11:65639800-65640600	Active TSS	Pancreas	Pancrea
49	chr11:65639800-65640600	Active TSS	Rectal Smooth Muscle	rectum
50	chr11:65639800-65640600	Active TSS	HepG2	liver

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