Variant report

Variant	rs11553576
Chromosome Location	chr11:62378801-62378802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr11:62378676-62381116	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:62373812-62380351	K562	blood:	n/a	n/a
3	JUN	chr11:62378784-62381159	K562	blood:	n/a	chr11:62380596-62380605 chr11:62380682-62380692 chr11:62379883-62379892 chr11:62379887-62379896
4	ELF1	chr11:62378784-62381035	GM12878	blood:	n/a	chr11:62379951-62379963 chr11:62379953-62379962
5	MXI1	chr11:62378780-62380391	IMR90	lung:	n/a	n/a
6	HMGN3	chr11:62378634-62379056	K562	blood:	n/a	n/a
7	CTCF	chr11:62378776-62381440	SK-N-SH	brain:	n/a	chr11:62380048-62380066 chr11:62380083-62380099 chr11:62381391-62381404 chr11:62380085-62380098 chr11:62380082-62380100 chr11:62380051-62380064
8	MAX	chr11:62378734-62380723	K562	blood:	n/a	n/a
9	POLR2A	chr11:62378770-62380545	PFSK-1	brain:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62378551..62381260-chr11:62552189..62554776,3	K562	blood:
2	chr11:62377281..62381950-chr11:62571197..62574724,7	K562	blood:
3	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
4	chr11:62378546..62380116-chr11:62436360..62439103,2	MCF-7	breast:
5	chr11:62377842..62380816-chr11:62605555..62609086,5	K562	blood:
6	chr11:62377695..62382560-chr11:62411978..62415698,6	MCF-7	breast:
7	chr11:62378127..62383239-chr11:62606559..62611171,5	K562	blood:
8	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
9	chr11:62339264..62341444-chr11:62378101..62380412,2	MCF-7	breast:
10	chr11:62377585..62379687-chr11:62554018..62556330,2	K562	blood:
11	chr11:62378546..62380090-chr11:62458877..62460420,2	K562	blood:
12	chr11:62377536..62380529-chr11:62493370..62497128,3	K562	blood:
13	chr11:62355644..62361752-chr11:62377047..62383949,17	MCF-7	breast:
14	chr11:62378641..62383731-chr11:62412268..62415992,8	K562	blood:
15	chr11:62377060..62379469-chr11:62472700..62475103,2	K562	blood:
16	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
17	chr11:62378127..62382168-chr11:62606723..62610399,5	MCF-7	breast:
18	chr11:62312633..62315593-chr11:62378252..62381432,4	MCF-7	breast:
19	chr11:62376924..62380375-chr11:62537380..62541874,4	K562	blood:
20	chr11:62377568..62383566-chr11:62416977..62422354,8	K562	blood:
21	chr11:62378061..62382695-chr11:62418790..62422319,4	MCF-7	breast:
22	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:
23	chr11:62378763..62382397-chr11:62538915..62541537,3	K562	blood:

No data

Variant related genes	Relation type
ROM1	TF binding region
EML3	TF binding region
ENSG00000255432	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000257058	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000255508	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1061093	0.81[EUR][1000 genomes]
rs11231138	0.96[CEU][hapmap]
rs11231141	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11231144	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs11231145	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231150	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231151	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231152	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231154	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231155	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11231156	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11231161	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12049914	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12225213	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12808829	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17773169	0.96[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs1801144	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2428548	0.92[CEU][hapmap]
rs2428549	0.92[CEU][hapmap]
rs2428551	0.82[EUR][1000 genomes]
rs2509961	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs2509982	0.92[CEU][hapmap]
rs2512562	0.92[CEU][hapmap]
rs2512563	0.96[CEU][hapmap]
rs2516633	0.92[GIH][hapmap];0.80[TSI][hapmap]
rs2516634	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2849030	1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2849031	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs34894392	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35156678	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs35880596	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58720921	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61296092	0.82[EUR][1000 genomes]
rs67308910	0.80[AMR][1000 genomes]
rs7124057	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71490390	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71490394	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72927213	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7928833	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7930896	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs7937146	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7943191	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
7	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
8	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
9	nsv897622	chr11:62366986-62392229	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11553576	EML3	cis	Esophagus Mucosa	GTEx
rs11553576	CFL1	cis	parietal	SCAN
rs11553576	C11orf48	cis	cerebellum	SCAN
rs11553576	MTA2	cis	Esophagus Mucosa	GTEx
rs11553576	EML3	cis	cerebellum	SCAN
rs11553576	TUT1	cis	parietal	SCAN
rs11553576	EEF1G	cis	multi-tissue	Pritchard
rs11553576	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11553576	SLC22A25	cis	parietal	SCAN
rs11553576	SCYL1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62370200-62379000	Weak transcription	Fetal Kidney	kidney
2	chr11:62371000-62379000	Weak transcription	Fetal Brain Female	brain
3	chr11:62371600-62379000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:62374600-62379400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:62375400-62379800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:62376800-62379000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:62377400-62379000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr11:62377800-62379200	Genic enhancers	Spleen	Spleen
9	chr11:62378000-62379000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:62378000-62379000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:62378000-62379000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:62378000-62379000	Genic enhancers	Fetal Muscle Leg	muscle
13	chr11:62378200-62379000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:62378200-62379000	Genic enhancers	Fetal Intestine Small	intestine
15	chr11:62378200-62379000	Enhancers	Fetal Lung	lung
16	chr11:62378200-62379000	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr11:62378200-62379000	Genic enhancers	Fetal Stomach	stomach
18	chr11:62378200-62379000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr11:62378400-62379000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:62378400-62379000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr11:62378400-62379000	Enhancers	Primary B cells from cord blood	blood
22	chr11:62378400-62379000	Enhancers	Primary hematopoietic stem cells	blood
23	chr11:62378400-62379000	Enhancers	Fetal Heart	heart
24	chr11:62378400-62379000	Enhancers	Left Ventricle	heart
25	chr11:62378400-62379000	Enhancers	Ovary	ovary
26	chr11:62378400-62379000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr11:62378400-62379000	Flanking Active TSS	GM12878-XiMat	blood
28	chr11:62378400-62379000	Flanking Active TSS	HepG2	liver
29	chr11:62378400-62379200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:62378400-62379200	Enhancers	Stomach Mucosa	stomach
31	chr11:62378400-62379800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr11:62378400-62379800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr11:62378600-62379000	Enhancers	Brain Angular Gyrus	brain
34	chr11:62378600-62379000	Enhancers	Colon Smooth Muscle	Colon
35	chr11:62378600-62379000	Enhancers	Fetal Intestine Large	intestine
36	chr11:62378600-62379000	Enhancers	Fetal Thymus	thymus
37	chr11:62378600-62379000	Enhancers	Lung	lung
38	chr11:62378600-62379000	Enhancers	Psoas Muscle	Psoas
39	chr11:62378600-62379000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr11:62378600-62379000	Enhancers	Small Intestine	intestine
41	chr11:62378600-62379000	Enhancers	NHDF-Ad	bronchial
42	chr11:62378600-62379200	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr11:62378600-62379200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:62378600-62379200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:62378600-62379200	Flanking Active TSS	A549	lung
46	chr11:62378600-62379200	Flanking Active TSS	HSMM	muscle
47	chr11:62378600-62379400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr11:62378600-62379400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:62378600-62379400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:62378600-62379400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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