Variant report

Variant	rs11235965
Chromosome Location	chr11:73706291-73706292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:73706194-73706705	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:73706226-73706674	GM12878	blood:	n/a	n/a
3	SPI1	chr11:73706224-73706653	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:73706236-73706645	GM12891	blood:	n/a	n/a
5	TBP	chr11:73706125-73706800	GM12878	blood:	n/a	n/a
6	TAF1	chr11:73706226-73706657	GM12878	blood:	n/a	n/a
7	IKZF1	chr11:73706183-73707103	GM12878	blood:	n/a	n/a
8	EP300	chr11:73706187-73706587	GM12878	blood:	n/a	chr11:73706454-73706463
9	RUNX3	chr11:73706163-73707342	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:73706267-73707097	Raji	blood:	n/a	n/a
11	ELF1	chr11:73706221-73706630	K562	blood:	n/a	chr11:73706451-73706464
12	SPI1	chr11:73706244-73706561	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:73706238-73706715	GM12891	blood:	n/a	n/a
14	SMC3	chr11:73706253-73706488	GM12878	blood:	n/a	n/a
15	STAT3	chr11:73706179-73706856	GM12878	blood:	n/a	chr11:73706457-73706464
16	RUNX3	chr11:73706227-73707245	GM12878	blood:	n/a	n/a
17	RCOR1	chr11:73706287-73706526	K562	blood:	n/a	n/a
18	POLR2A	chr11:73706198-73706629	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:73706237-73706676	GM12891	blood:	n/a	n/a
20	EP300	chr11:73706277-73706558	GM12878	blood:	n/a	chr11:73706454-73706463
21	BATF	chr11:73706289-73706580	GM12878	blood:	n/a	n/a
22	BHLHE40	chr11:73706193-73706612	GM12878	blood:	n/a	n/a
23	EP300	chr11:73706237-73707176	GM12878	blood:	n/a	chr11:73706454-73706463
24	SPI1	chr11:73706202-73706572	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73691320..73695538-chr11:73704392..73710067,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UCP3-1	chr11:73706017-73707196	NONHSAT022872

Variant related genes	Relation type
ENSG00000256189	TF binding region
ENSG00000175567	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10898961	0.83[JPT][hapmap]
rs10898963	0.83[JPT][hapmap]
rs11235971	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11235972	0.87[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11600314	0.83[JPT][hapmap]
rs11602451	0.83[JPT][hapmap]
rs11607335	0.80[JPT][hapmap]
rs1565125	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1685333	0.83[JPT][hapmap];0.92[TSI][hapmap]
rs1800006	0.88[JPT][hapmap]
rs1800849	0.87[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2075576	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3741135	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814724	0.83[JPT][hapmap]
rs4539349	0.83[JPT][hapmap]
rs59900762	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619631	0.82[ASN][1000 genomes]
rs643064	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs649446	0.81[ASN][1000 genomes]
rs680786	0.82[ASN][1000 genomes]
rs681826	0.82[ASN][1000 genomes]
rs7109266	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs7930460	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11235965	ANO1	cis	cerebellum	SCAN
rs11235965	PPME1	cis	cerebellum	SCAN
rs11235965	PAAF1	cis	lymphoblastoid	seeQTL
rs11235965	FOLR3	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73695200-73711000	Weak transcription	Fetal Intestine Small	intestine
2	chr11:73702000-73711800	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:73702200-73706400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr11:73702200-73706400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:73702600-73706400	Weak transcription	Fetal Thymus	thymus
6	chr11:73702600-73711800	Weak transcription	Spleen	Spleen
7	chr11:73702800-73708600	Weak transcription	K562	blood
8	chr11:73702800-73711400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:73703000-73710000	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:73703000-73719400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:73703800-73706400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:73704000-73706600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr11:73704000-73709000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:73704600-73706600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:73704800-73706400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr11:73705200-73706400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:73705200-73707400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:73705400-73706400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr11:73705800-73706400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr11:73705800-73706800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr11:73705800-73707000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr11:73705800-73707400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:73705800-73707400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr11:73705800-73707400	Enhancers	Dnd41	blood
25	chr11:73705800-73708200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:73706000-73707000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr11:73706000-73707000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:73706000-73707200	Active TSS	Primary T cells fromperipheralblood	blood
29	chr11:73706000-73707200	Enhancers	Primary hematopoietic stem cells	blood
30	chr11:73706000-73707200	Flanking Active TSS	GM12878-XiMat	blood
31	chr11:73706000-73713800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:73706200-73706600	Active TSS	Primary B cells from cord blood	blood
33	chr11:73706200-73706600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:73706200-73707200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:73706200-73707600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr11:73706200-73707600	Enhancers	Thymus	Thymus

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