Variant report

Variant	rs12422015
Chromosome Location	chr11:57193653-57193654
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	POLR2A	chr11:57191261-57195084	K562	blood:	n/a	n/a
2	MAX	chr11:57192105-57195056	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
3	POLR2A	chr11:57191114-57195043	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:57191115-57195177	GM12892	blood:	n/a	n/a
5	UBTF	chr11:57193645-57193861	K562	blood:	n/a	n/a
6	MAX	chr11:57191980-57195156	K562	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
7	MTA3	chr11:57191526-57195524	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:57191591-57194992	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:57193648-57194922	K562	blood:	n/a	n/a
10	POLR2A	chr11:57191113-57195429	HL-60	blood:	n/a	n/a
11	MYC	chr11:57193487-57194164	K562	blood:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
12	POLR2A	chr11:57192189-57195457	Raji	blood:	n/a	n/a
13	RCOR1	chr11:57192103-57194085	IMR90	lung:	n/a	n/a
14	POLR2A	chr11:57191441-57195068	GM18526	blood:	n/a	n/a
15	POLR2A	chr11:57192099-57194232	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:57193531-57194118	U87	brain:	n/a	n/a
17	MTA3	chr11:57191939-57194306	GM12878	blood:	n/a	n/a
18	MYC	chr11:57192097-57195095	NB4	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
19	MYC	chr11:57192128-57194621	K562	blood:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
20	PML	chr11:57191892-57195093	GM12878	blood:	n/a	chr11:57192441-57192450
21	MYC	chr11:57193535-57193702	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr11:57191153-57195123	GM12891	blood:	n/a	n/a
23	POLR2A	chr11:57192095-57194977	NB4	blood:	n/a	n/a
24	NR2F2	chr11:57193165-57194182	K562	blood:	n/a	n/a
25	POLR2A	chr11:57191285-57195328	K562	blood:	n/a	n/a
26	POLR2A	chr11:57192131-57195018	GM15510	blood:	n/a	n/a
27	RUNX3	chr11:57192047-57195167	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:57191219-57194857	GM12891	blood:	n/a	n/a
29	POLR2A	chr11:57191596-57193776	K562	blood:	n/a	n/a
30	MYC	chr11:57192188-57195515	MCF10A-Er-Src	breast:	n/a	chr11:57193991-57194004 chr11:57192303-57192313 chr11:57193410-57193419 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193409-57193420 chr11:57193409-57193420 chr11:57193993-57194003 chr11:57192755-57192766 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57192440-57192449 chr11:57193992-57194001 chr11:57193409-57193420 chr11:57192754-57192769 chr11:57193992-57194003 chr11:57193992-57194003
31	MAX	chr11:57193464-57194850	H1-hESC	embryonic stem cell:	n/a	chr11:57193991-57194004 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194002 chr11:57193993-57194002 chr11:57193992-57194003 chr11:57193993-57194003 chr11:57193993-57194002 chr11:57193991-57194004 chr11:57193993-57194003 chr11:57193992-57194003 chr11:57193991-57194006 chr11:57193992-57194001 chr11:57193992-57194003 chr11:57193992-57194003
32	YY1	chr11:57193474-57193904	K562	blood:	n/a	n/a
33	POLR2A	chr11:57192079-57195002	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:57191305-57194984	GM12878	blood:	n/a	n/a
35	SIN3A	chr11:57193477-57193787	GM12878	blood:	n/a	n/a
36	WRNIP1	chr11:57191369-57195127	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:57193412-57193687	HUVEC	blood vessel:	n/a	n/a
38	HCFC1	chr11:57193653-57193662	K562	blood:	n/a	n/a
39	POLR2A	chr11:57191179-57195028	K562	blood:	n/a	n/a
40	POLR2A	chr11:57191196-57195715	U87	brain:	n/a	n/a
41	YY1	chr11:57193520-57193770	K562	blood:	n/a	n/a
42	USF1	chr11:57193377-57193754	K562	blood:	n/a	n/a
43	POLR2A	chr11:57191294-57195046	GM12892	blood:	n/a	n/a
44	POLR2A	chr11:57193524-57194315	GM12891	blood:	n/a	n/a
45	E2F6	chr11:57192150-57195054	K562	blood:	n/a	chr11:57192552-57192561 chr11:57194364-57194373 chr11:57193865-57193872 chr11:57193865-57193872 chr11:57193865-57193872
46	USF2	chr11:57192132-57194876	GM12878	blood:	n/a	chr11:57192756-57192765 chr11:57192756-57192765 chr11:57194437-57194453 chr11:57192875-57192891 chr11:57192755-57192766
47	TEAD4	chr11:57193352-57193999	K562	blood:	n/a	n/a
48	JUN	chr11:57191735-57195179	K562	blood:	n/a	chr11:57193429-57193438 chr11:57191781-57191790 chr11:57192574-57192583 chr11:57192438-57192450 chr11:57192440-57192448 chr11:57194900-57194911
49	YY1	chr11:57193450-57194119	GM12892	blood:	n/a	n/a
50	RELA	chr11:57191848-57195185	GM18951	blood:	n/a	chr11:57192456-57192465 chr11:57192456-57192465

No.	Distal block	Cell Line	Cell type
1	chr11:57092537..57094239-chr11:57192344..57194712,2	K562	blood:
2	chr11:57191864..57193854-chr11:57413705..57415355,2	K562	blood:
3	chr11:57190585..57193869-chr11:57296385..57298665,4	K562	blood:
4	chr11:57191864..57194047-chr11:57412922..57415205,2	K562	blood:
5	chr11:57190585..57194081-chr11:57295965..57298665,6	K562	blood:
6	chr11:57192480..57194732-chr11:57434843..57437661,2	K562	blood:
7	chr11:57094351..57096693-chr11:57193203..57197242,3	K562	blood:

Variant related genes	Relation type
SLC43A3	TF binding region
ENSG00000254979	TF binding region
ENSG00000238692	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000254662	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11229028	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11820985	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11822095	1.00[ASN][1000 genomes]
rs11822910	0.98[ASN][1000 genomes]
rs11827928	0.98[ASN][1000 genomes]
rs11828218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12788236	0.81[ASN][1000 genomes]
rs2250887	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439448	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581924	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581927	0.81[EUR][1000 genomes]
rs2581928	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584858	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729389	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2729392	0.81[EUR][1000 genomes]
rs4477456	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4529894	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60961847	0.91[ASN][1000 genomes]
rs61886978	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106223	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7122734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12422015	CTNND1	cis	cerebellum	SCAN
rs12422015	DTX4	cis	cerebellum	SCAN
rs12422015	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs12422015	OR5AP2	cis	parietal	SCAN
rs12422015	OR5AR1	cis	parietal	SCAN
rs12422015	OR5T3	cis	parietal	SCAN
rs12422015	TIMM10	cis	cerebellum	SCAN
rs12422015	TIMM10	cis	parietal	SCAN
rs12422015	SLC43A3	cis	cerebellum	SCAN
rs12422015	OR8U1	cis	cerebellum	SCAN
rs12422015	SLC43A1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57185600-57193800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57186000-57194000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:57188600-57193800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:57189800-57194000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr11:57191200-57194000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr11:57191200-57194400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:57191400-57193800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr11:57191400-57194000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
9	chr11:57191400-57194000	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr11:57191400-57194200	Transcr. at gene 5' and 3'	K562	blood
11	chr11:57191600-57193800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:57191600-57193800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:57191600-57193800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:57191600-57193800	Enhancers	Fetal Brain Male	brain
15	chr11:57191600-57194000	Enhancers	Ovary	ovary
16	chr11:57191600-57194200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:57191600-57195200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:57191600-57195600	Enhancers	Spleen	Spleen
19	chr11:57191800-57193800	Enhancers	Primary B cells from cord blood	blood
20	chr11:57191800-57193800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:57191800-57193800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:57191800-57194000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:57191800-57194000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr11:57191800-57194200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:57191800-57194200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:57191800-57194200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr11:57191800-57194200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:57191800-57194800	Enhancers	Fetal Heart	heart
29	chr11:57191800-57195000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:57191800-57195000	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:57191800-57195000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr11:57191800-57195200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr11:57192000-57193800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:57192000-57193800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
35	chr11:57192000-57194000	Enhancers	Lung	lung
36	chr11:57192000-57194000	Enhancers	HSMMtube	muscle
37	chr11:57192000-57194200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr11:57192000-57194200	Flanking Active TSS	Liver	Liver
39	chr11:57192000-57194400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr11:57192000-57194600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr11:57192000-57195000	Flanking Active TSS	Fetal Thymus	thymus
42	chr11:57192200-57194000	Enhancers	Primary B cells from peripheral blood	blood
43	chr11:57192200-57194200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr11:57192200-57194200	Enhancers	Brain Substantia Nigra	brain
45	chr11:57192200-57195000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr11:57192200-57195000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr11:57192200-57195200	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr11:57192200-57195400	Flanking Active TSS	Osteobl	bone
49	chr11:57192400-57193800	Enhancers	Aorta	Aorta
50	chr11:57192400-57194000	Genic enhancers	Fetal Intestine Small	intestine

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