Variant report

Variant	rs11227302
Chromosome Location	chr11:65554502-65554503
allele	A/G
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	MAX	chr11:65553761-65555125	ECC-1	luminal epithelium:	n/a	chr11:65554464-65554474 chr11:65554157-65554167
2	ZEB1	chr11:65554329-65554945	GM12878	blood:	n/a	chr11:65554615-65554626
3	POLR2A	chr11:65554447-65554766	H1-neurons	neurons:	n/a	n/a
4	MAX	chr11:65553701-65555122	MCF-7	breast:	n/a	chr11:65554464-65554474 chr11:65554157-65554167
5	TEAD4	chr11:65554117-65554898	ECC-1	luminal epithelium:	n/a	n/a
6	E2F6	chr11:65554479-65555892	H1-hESC	embryonic stem cell:	n/a	chr11:65554555-65554564 chr11:65555196-65555205 chr11:65555197-65555212 chr11:65554553-65554563 chr11:65555353-65555362 chr11:65555353-65555365 chr11:65554603-65554612
7	NFIC	chr11:65553857-65554853	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr11:65554206-65554808	HCT-116	colon:	n/a	n/a
9	MAX	chr11:65553717-65556062	H1-hESC	embryonic stem cell:	n/a	chr11:65554464-65554474 chr11:65555943-65555953 chr11:65555243-65555253 chr11:65554157-65554167 chr11:65555486-65555495
10	POLR2A	chr11:65554435-65554769	ECC-1	luminal epithelium:	n/a	n/a
11	NR2F2	chr11:65553895-65554609	MCF-7	breast:	n/a	n/a
12	MAX	chr11:65553767-65555136	ECC-1	luminal epithelium:	n/a	chr11:65554464-65554474 chr11:65554157-65554167
13	SIN3AK20	chr11:65554103-65554979	HCT-116	colon:	n/a	n/a
14	GATA3	chr11:65553847-65554829	MCF-7	breast:	n/a	chr11:65553964-65553972
15	TAF1	chr11:65554433-65554715	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr11:65554001-65555003	HCT-116	colon:	n/a	n/a
17	ZBTB7A	chr11:65553850-65554572	ECC-1	luminal epithelium:	n/a	n/a
18	TAF1	chr11:65554457-65554706	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3AK20	chr11:65553765-65556882	MCF-7	breast:	n/a	n/a
20	MAX	chr11:65553720-65554983	MCF-7	breast:	n/a	chr11:65554464-65554474 chr11:65554157-65554167
21	NRF1	chr11:65554231-65554535	H1-hESC	embryonic stem cell:	n/a	chr11:65554396-65554407 chr11:65554398-65554407 chr11:65554393-65554407
22	FOXA1	chr11:65554283-65554527	T-47D	breast:	n/a	n/a
23	POLR2A	chr11:65554363-65554849	HCT-116	colon:	n/a	n/a
24	POLR2A	chr11:65554491-65554744	H1-neurons	neurons:	n/a	n/a
25	GATA3	chr11:65553720-65554930	MCF-7	breast:	n/a	chr11:65553964-65553972
26	HDAC2	chr11:65553811-65555066	MCF-7	breast:	n/a	n/a
27	HDAC2	chr11:65553909-65554954	MCF-7	breast:	n/a	n/a
28	SIN3AK20	chr11:65553762-65554973	MCF-7	breast:	n/a	n/a
29	POLR2A	chr11:65554320-65554859	ProgFib	skin:	n/a	n/a
30	POLR2A	chr11:65554469-65554699	ECC-1	luminal epithelium:	n/a	n/a
31	TEAD4	chr11:65554475-65554807	H1-hESC	embryonic stem cell:	n/a	n/a
32	PML	chr11:65554331-65554836	MCF-7	breast:	n/a	n/a
33	TAF1	chr11:65554285-65554913	MCF-7	breast:	n/a	n/a
34	GATA3	chr11:65554177-65554696	T-47D	breast:	n/a	n/a
35	POLR2A	chr11:65554295-65554912	MCF-7	breast:	n/a	n/a
36	TCF12	chr11:65554045-65554751	ECC-1	luminal epithelium:	n/a	n/a
37	TEAD4	chr11:65554132-65554874	ECC-1	luminal epithelium:	n/a	n/a
38	NR2F2	chr11:65553808-65554765	MCF-7	breast:	n/a	n/a
39	TCF12	chr11:65553852-65555011	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr11:65554272-65554957	MCF-7	breast:	n/a	n/a
41	POLR2A	chr11:65554199-65555019	MCF-7	breast:	n/a	n/a
42	ELF1	chr11:65554103-65555120	MCF-7	breast:	n/a	chr11:65554979-65554988 chr11:65554230-65554242 chr11:65554468-65554480 chr11:65554165-65554177
43	MYC	chr11:65554242-65554743	MCF-7	breast:	n/a	chr11:65554464-65554474
44	YY1	chr11:65554474-65554719	HCT-116	colon:	n/a	chr11:65554555-65554564 chr11:65554603-65554612 chr11:65554553-65554564

No.	Distal block	Cell Line	Cell type
1	chr11:65552279..65555050-chr11:65558664..65561977,4	K562	blood:
2	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:
3	chr11:65381719..65383349-chr11:65554196..65557028,2	MCF-7	breast:
4	chr11:65428991..65430722-chr11:65553054..65555889,2	MCF-7	breast:
5	chr11:65553824..65556845-chr11:65623477..65626342,3	K562	blood:
6	chr11:65479523..65484500-chr11:65551483..65556601,5	MCF-7	breast:
7	chr11:65552272..65555849-chr11:65684886..65688039,3	MCF-7	breast:
8	chr11:65552282..65556398-chr11:65623209..65626538,5	MCF-7	breast:
9	chr11:65545987..65548666-chr11:65554230..65557097,2	K562	blood:
10	chr11:65551697..65554555-chr11:65655334..65658299,2	K562	blood:

Variant related genes	Relation type
OVOL1	TF binding region
ENSG00000175827	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000254470	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000197136	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227261	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs11227283	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11227284	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227288	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11227303	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1151488	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs1193851	0.85[CHB][hapmap]
rs1205259	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs12273982	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12287832	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1784223	0.85[CHB][hapmap]
rs1787034	0.85[CHB][hapmap];0.94[CHD][hapmap]
rs3372	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs4930304	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs494003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs578056	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7122657	0.85[CHB][hapmap]
rs7944860	0.85[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv897759	chr11:65543827-65554502	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv897760	chr11:65545306-65559266	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv3321581	chr11:65552901-65555749	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11227302	SLC22A24	cis	parietal	SCAN
rs11227302	SNX32	cis	cerebellum	SCAN
rs11227302	KCNK4	cis	cerebellum	SCAN
rs11227302	SNX32	cis	parietal	SCAN
rs11227302	IZUMO2	trans	parietal	SCAN
rs11227302	RNASEH2C	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65551200-65555600	Bivalent Enhancer	Fetal Thymus	thymus
2	chr11:65552800-65554600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
3	chr11:65553400-65554600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:65553400-65554600	Enhancers	Gastric	stomach
5	chr11:65553400-65555200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr11:65553400-65555800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr11:65553400-65556400	Bivalent Enhancer	Spleen	Spleen
8	chr11:65553400-65557200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr11:65553600-65554600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr11:65553600-65554600	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr11:65553600-65554600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
12	chr11:65553600-65555000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr11:65553600-65555600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr11:65553600-65556000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr11:65553600-65556000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:65553600-65556000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr11:65553600-65556000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr11:65553600-65556000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr11:65553800-65554600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr11:65553800-65554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:65553800-65554600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr11:65553800-65554600	Active TSS	Esophagus	oesophagus
23	chr11:65553800-65554600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr11:65553800-65554800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
25	chr11:65553800-65555000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:65553800-65555000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:65553800-65555200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr11:65553800-65556000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr11:65553800-65556200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:65554000-65554600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr11:65554000-65554600	Active TSS	Duodenum Mucosa	Duodenum
32	chr11:65554000-65554600	Bivalent Enhancer	Placenta	Placenta
33	chr11:65554000-65555000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
34	chr11:65554000-65555000	Bivalent Enhancer	Left Ventricle	heart
35	chr11:65554000-65555000	Flanking Active TSS	HMEC	breast
36	chr11:65554000-65555200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:65554000-65555600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:65554000-65555600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr11:65554000-65555800	Flanking Bivalent TSS/Enh	Thymus	Thymus
40	chr11:65554000-65556000	Bivalent Enhancer	Fetal Brain Male	brain
41	chr11:65554000-65556000	Enhancers	Lung	lung
42	chr11:65554000-65556200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:65554000-65556200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr11:65554000-65556200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr11:65554200-65554600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:65554200-65554600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:65554200-65554600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:65554200-65554600	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr11:65554200-65554600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
50	chr11:65554200-65554600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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