Variant report

Variant	rs11231161
Chromosome Location	chr11:62378221-62378222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:62377887-62378296	K562	blood:	n/a	n/a
2	POLR2A	chr11:62373812-62380351	K562	blood:	n/a	n/a
3	CBX3	chr11:62377889-62378275	K562	blood:	n/a	n/a
4	CEBPB	chr11:62378107-62378386	K562	blood:	n/a	n/a
5	CEBPB	chr11:62377982-62378378	K562	blood:	n/a	n/a
6	CEBPB	chr11:62378113-62378279	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:62377907-62378762	K562	blood:	n/a	n/a
8	ZNF143	chr11:62377913-62378231	K562	blood:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62377281..62381950-chr11:62571197..62574724,7	K562	blood:
2	chr11:62373213..62384382-chr11:62430946..62441432,32	K562	blood:
3	chr11:62377842..62380816-chr11:62605555..62609086,5	K562	blood:
4	chr11:62377695..62382560-chr11:62411978..62415698,6	MCF-7	breast:
5	chr11:62378127..62383239-chr11:62606559..62611171,5	K562	blood:
6	chr11:62373213..62382341-chr11:62430187..62440422,29	K562	blood:
7	chr11:62339264..62341444-chr11:62378101..62380412,2	MCF-7	breast:
8	chr11:62377585..62379687-chr11:62554018..62556330,2	K562	blood:
9	chr11:62374418..62378633-chr11:62387946..62390795,5	MCF-7	breast:
10	chr11:62377536..62380529-chr11:62493370..62497128,3	K562	blood:
11	chr11:62355644..62361752-chr11:62377047..62383949,17	MCF-7	breast:
12	chr11:62377060..62379469-chr11:62472700..62475103,2	K562	blood:
13	chr11:62375885..62391030-chr11:62428132..62435550,30	MCF-7	breast:
14	chr11:62378127..62382168-chr11:62606723..62610399,5	MCF-7	breast:
15	chr11:62376924..62380375-chr11:62537380..62541874,4	K562	blood:
16	chr11:62377568..62383566-chr11:62416977..62422354,8	K562	blood:
17	chr11:62378061..62382695-chr11:62418790..62422319,4	MCF-7	breast:
18	chr11:62373062..62383315-chr11:62429730..62439835,25	MCF-7	breast:

No data

Variant related genes	Relation type
ROM1	TF binding region
EML3	TF binding region
ENSG00000162231	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000162222	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1061093	0.85[EUR][1000 genomes]
rs10792356	0.82[JPT][hapmap]
rs10897289	0.82[JPT][hapmap]
rs11231138	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11231141	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11231144	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11231145	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11231150	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231151	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231152	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231154	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231155	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11231156	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231182	0.82[JPT][hapmap]
rs11553576	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	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12223627	0.81[ASN][1000 genomes]
rs12225213	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12226821	0.81[ASN][1000 genomes]
rs12808829	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13941	1.00[JPT][hapmap]
rs17773169	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes]
rs1801144	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2428548	0.92[CEU][hapmap]
rs2428549	0.92[CEU][hapmap]
rs2428551	0.85[EUR][1000 genomes]
rs2509961	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap]
rs2509982	0.92[CEU][hapmap]
rs2512562	0.92[CEU][hapmap]
rs2512563	0.96[CEU][hapmap]
rs2516633	0.88[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs2516634	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2849030	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2849031	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2956993	0.82[JPT][hapmap]
rs3018561	0.82[JPT][hapmap]
rs34065644	0.81[ASN][1000 genomes]
rs34894392	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35156678	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs35587183	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs35880596	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3809079	0.82[JPT][hapmap]
rs3923805	0.81[ASN][1000 genomes]
rs489778	0.82[JPT][hapmap]
rs58720921	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs597259	1.00[JPT][hapmap]
rs61296092	0.85[EUR][1000 genomes]
rs644616	0.82[JPT][hapmap]
rs67308910	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs693698	0.82[JPT][hapmap]
rs7124057	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71490390	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71490392	0.80[EUR][1000 genomes]
rs71490394	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72927213	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928833	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7930896	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7937146	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7943191	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7949030	0.82[JPT][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11231161	EML3	cis	cerebellum	SCAN
rs11231161	EEF1G	cis	multi-tissue	Pritchard
rs11231161	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11231161	EML3	cis	multi-tissue	Pritchard
rs11231161	EML3	cis	Esophagus Mucosa	GTEx
rs11231161	SLC22A25	cis	parietal	SCAN
rs11231161	TUT1	cis	parietal	SCAN
rs11231161	SCYL1	cis	parietal	SCAN
rs11231161	SLC22A9	cis	parietal	SCAN
rs11231161	MTA2	cis	Esophagus Mucosa	GTEx
rs11231161	C11orf48	cis	cerebellum	SCAN
rs11231161	CFL1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62370000-62378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:62370200-62379000	Weak transcription	Fetal Kidney	kidney
3	chr11:62370600-62378600	Weak transcription	Small Intestine	intestine
4	chr11:62370600-62378800	Weak transcription	HSMMtube	muscle
5	chr11:62370800-62378400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:62370800-62378400	Weak transcription	Left Ventricle	heart
7	chr11:62370800-62378600	Weak transcription	Psoas Muscle	Psoas
8	chr11:62370800-62378600	Weak transcription	Right Atrium	heart
9	chr11:62371000-62378400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:62371000-62378600	Strong transcription	Osteobl	bone
11	chr11:62371000-62378800	Weak transcription	Brain Germinal Matrix	brain
12	chr11:62371000-62379000	Weak transcription	Fetal Brain Female	brain
13	chr11:62371200-62378400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:62371400-62378400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:62371600-62378400	Weak transcription	Stomach Mucosa	stomach
16	chr11:62371600-62379000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:62371800-62378800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:62372600-62378800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:62372800-62378400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:62372800-62378600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:62373000-62378400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:62373000-62378400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:62373000-62378600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:62373600-62378400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:62373800-62378400	Weak transcription	Primary B cells from cord blood	blood
26	chr11:62373800-62378600	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:62374600-62378400	Weak transcription	Fetal Heart	heart
28	chr11:62374600-62379400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:62374800-62378400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:62375000-62378400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:62375000-62378400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:62375200-62378400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:62375200-62378600	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr11:62375200-62378800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr11:62375400-62378600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:62375400-62379800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:62375600-62378600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr11:62375800-62378600	Weak transcription	NHDF-Ad	bronchial
39	chr11:62376000-62378400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:62376000-62378600	Weak transcription	HSMM	muscle
41	chr11:62376000-62378800	Weak transcription	NH-A	brain
42	chr11:62376200-62378800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:62376200-62378800	Weak transcription	Aorta	Aorta
44	chr11:62376400-62378800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:62376400-62378800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:62376600-62378400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:62376600-62378400	Strong transcription	Fetal Thymus	thymus
48	chr11:62376800-62378400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr11:62376800-62378600	Weak transcription	Brain Angular Gyrus	brain
50	chr11:62376800-62379000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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