Variant report

Variant	rs2736533
Chromosome Location	chr11:5410103-5410104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr11:5409907-5410185	H1-hESC	embryonic stem cell:	n/a	chr11:5409990-5410001
2	JUND	chr11:5409905-5410122	HepG2	liver:	n/a	chr11:5409990-5410001

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:5410053-5410103	GM19239	blood:	n/a
2	chr11:5410053-5410103	GM12891	blood:	n/a
3	chr11:5410053-5410103	HRE	kidney:	n/a
4	chr11:5410053-5410103	NT2-D1	testis:	n/a
5	chr11:5410053-5410103	HCT-116	colon:	n/a
6	chr11:5410053-5410103	HCF	heart:	n/a
7	chr11:5410053-5410103	MCF10A-Er-Src	breast:	n/a
8	chr11:5410053-5410103	MCF-7	breast:	n/a
9	chr11:5410053-5410103	HMEC	breast:	n/a
10	chr11:5410053-5410103	AG10803	skin:	n/a
11	chr11:5410053-5410103	SK-N-MC	brain:	n/a
12	chr11:5410053-5410103	T-47D	breast:	n/a
13	chr11:5410053-5410103	GM12892	blood:	n/a
14	chr11:5410053-5410103	GM12878	blood:	n/a
15	chr11:5410053-5410103	BJ	skin:	n/a
16	chr11:5410053-5410103	NH-A	brain:	n/a
17	chr11:5410053-5410103	PrEC	prostate:	n/a
18	chr11:5410053-5410103	SK-N-SH_RA	brain:	n/a
19	chr11:5410053-5410103	Caco-2	colon:	n/a
20	chr11:5410053-5410103	SKMC	muscle:	n/a
21	chr11:5410053-5410103	U87	brain:	n/a
22	chr11:5410053-5410103	ProgFib	skin:	n/a
23	chr11:5410053-5410103	AG09309	skin:	n/a
24	chr11:5410053-5410103	HepG2	liver:	n/a
25	chr11:5410053-5410103	K562	blood:	n/a
26	chr11:5410053-5410103	GM06990	blood:	n/a
27	chr11:5410053-5410103	LNCaP	prostate:	n/a
28	chr11:5410053-5410103	SK-N-SH	brain:	n/a
29	chr11:5410053-5410103	ECC-1	luminal epithelium:	n/a
30	chr11:5410053-5410103	NB4	blood:	n/a
31	chr11:5410053-5410103	HCPEpiC	choroid plexus:	n/a
32	chr11:5410053-5410103	HIPEpiC	eye:	n/a
33	chr11:5410053-5410103	HPAEpiC	pulmonary alveolar:	n/a
34	chr11:5410053-5410103	AG09319	gingival:	n/a
35	chr11:5410053-5410103	AG04449	skin:	fetal
36	chr11:5410053-5410103	AG04450	lung:	fetal
37	chr11:5410053-5410103	NHBE	bronchial:	n/a
38	chr11:5410053-5410103	RPTEC	kidney:	n/a
39	chr11:5410053-5410103	HUVEC	blood vessel:	n/a
40	chr11:5410053-5410103	AoSMC	blood vessel:	n/a
41	chr11:5410053-5410103	PANC-1	pancreas:	n/a
42	chr11:5410053-5410103	Hela-S3	cervix:	n/a
43	chr11:5410053-5410103	HRCEpiC	kidney:	n/a
44	chr11:5410053-5410103	IMR90	lung:	fetal
45	chr11:5410053-5410103	BE2_C	brain:	n/a
46	chr11:5410053-5410103	Hepatocyte	liver:	n/a
47	chr11:5410053-5410103	PFSK-1	brain:	n/a
48	chr11:5410053-5410103	CMK	blood:	n/a
49	chr11:5410053-5410103	ovcar-3	ovarian:	n/a
50	chr11:5410053-5410103	NHDF-neo	bronchial:	n/a

No data

Variant related genes	Relation type
OR51M1	TF binding region
OR51M1	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10500638	0.81[CEU][hapmap]
rs12802177	0.87[CEU][hapmap]
rs1391607	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546216	0.81[CEU][hapmap]
rs2340655	0.80[CEU][hapmap]
rs2647546	0.81[CEU][hapmap]
rs2647549	0.81[CEU][hapmap]
rs2647557	0.81[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2647583	0.82[YRI][hapmap]
rs2647610	0.89[CEU][hapmap]
rs2723372	0.81[CEU][hapmap]
rs2723373	0.84[CEU][hapmap]
rs2736521	0.81[YRI][hapmap]
rs2736530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736536	0.81[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs2736542	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs4910769	0.84[CEU][hapmap]
rs7113335	0.86[CEU][hapmap]
rs7116499	0.81[CEU][hapmap]
rs872163	0.82[YRI][hapmap]
rs872166	0.82[YRI][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	nsv524400	chr11:5328361-5416622	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1048608	chr11:5328516-5645179	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
3	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv896931	chr11:5357881-5505149	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv832057	chr11:5375585-5576200	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv896932	chr11:5392484-5424170	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
7	nsv1044243	chr11:5401036-5432316	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	nsv896933	chr11:5402315-5440620	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
9	esv2761646	chr11:5406123-5454241	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
10	esv18235	chr11:5409794-5412609	Enhancers Weak transcription Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
11	esv1846298	chr11:5410103-5431986	Enhancers Strong transcription Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2736533	TRIM66	cis	cerebellum	SCAN
rs2736533	OR52H1	cis	cerebellum	SCAN
rs2736533	TRIM68	cis	parietal	SCAN
rs2736533	SCUBE2	cis	parietal	SCAN
rs2736533	KRTAP5-2	cis	cerebellum	SCAN
rs2736533	OR56B1	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5406000-5410200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr11:5408400-5410200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr11:5408400-5410200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr11:5408400-5410400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr11:5408600-5410200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr11:5408800-5410600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr11:5409200-5410600	Weak transcription	K562	blood
8	chr11:5409600-5412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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