Variant report

Variant	rs2649667
Chromosome Location	chr11:57270509-57270510
allele	A/C
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	EP300	chr11:57270239-57270687	HepG2	liver:	n/a	n/a
2	RAD21	chr11:57270402-57270602	HepG2	liver:	n/a	n/a
3	SP1	chr11:57270242-57270744	HepG2	liver:	n/a	n/a
4	HDAC2	chr11:57270359-57270746	HepG2	liver:	n/a	n/a
5	CTCF	chr11:57270380-57270530	HepG2	liver:	n/a	n/a
6	HNF4A	chr11:57270270-57270592	HepG2	liver:	n/a	chr11:57270490-57270503 chr11:57270490-57270503 chr11:57270469-57270485 chr11:57270473-57270487 chr11:57270492-57270504 chr11:57270489-57270504
7	NFIC	chr11:57270333-57270689	HepG2	liver:	n/a	n/a
8	HNF4G	chr11:57270268-57270692	HepG2	liver:	n/a	chr11:57270490-57270503 chr11:57270490-57270503 chr11:57270469-57270485 chr11:57270488-57270503 chr11:57270473-57270487 chr11:57270492-57270504
9	POLR2A	chr11:57270451-57270524	K562	blood:	n/a	n/a
10	RCOR1	chr11:57270355-57270638	HepG2	liver:	n/a	n/a
11	FOXA1	chr11:57270251-57270745	HepG2	liver:	n/a	n/a
12	TEAD4	chr11:57270262-57270747	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:57270486-57270726	HepG2	liver:	n/a	n/a
14	NR3C1	chr11:57270365-57270840	A549	lung:	n/a	chr11:57270555-57270569 chr11:57270549-57270575
15	MYBL2	chr11:57270213-57270851	HepG2	liver:	n/a	n/a
16	SMC3	chr11:57270413-57270625	HepG2	liver:	n/a	n/a
17	JUND	chr11:57270381-57270612	HepG2	liver:	n/a	n/a
18	MXI1	chr11:57270385-57270677	HepG2	liver:	n/a	n/a
19	EP300	chr11:57270300-57270731	HepG2	liver:	n/a	n/a
20	MBD4	chr11:57270230-57270739	HepG2	liver:	n/a	n/a
21	FOXA2	chr11:57270298-57270741	HepG2	liver:	n/a	n/a
22	NR3C1	chr11:57270272-57270860	A549	lung:	n/a	chr11:57270555-57270569 chr11:57270549-57270575
23	MAFK	chr11:57270447-57270646	HepG2	liver:	n/a	chr11:57270596-57270611
24	ARID3A	chr11:57270363-57270634	HepG2	liver:	n/a	n/a
25	BHLHE40	chr11:57270408-57270603	HepG2	liver:	n/a	n/a
26	EP300	chr11:57270364-57270632	HepG2	liver:	n/a	n/a
27	FOXA1	chr11:57270221-57270837	HepG2	liver:	n/a	n/a
28	FOXA2	chr11:57270307-57271031	HepG2	liver:	n/a	n/a
29	NR2F2	chr11:57270358-57270706	MCF-7	breast:	n/a	chr11:57270492-57270507
30	POLR2A	chr11:57270373-57270687	HepG2	liver:	n/a	n/a
31	HNF4G	chr11:57270202-57270785	HepG2	liver:	n/a	chr11:57270490-57270503 chr11:57270490-57270503 chr11:57270469-57270485 chr11:57270488-57270503 chr11:57270473-57270487 chr11:57270492-57270504
32	NFIC	chr11:57270230-57270755	HepG2	liver:	n/a	n/a
33	RXRA	chr11:57270336-57270696	HepG2	liver:	n/a	chr11:57270495-57270504
34	MYBL2	chr11:57270263-57270766	HepG2	liver:	n/a	n/a
35	HDAC2	chr11:57270283-57270736	HepG2	liver:	n/a	n/a
36	HNF4A	chr11:57270359-57270640	HepG2	liver:	n/a	chr11:57270490-57270503 chr11:57270490-57270503 chr11:57270469-57270485 chr11:57270473-57270487 chr11:57270492-57270504 chr11:57270489-57270504
37	NR2F2	chr11:57270144-57270884	HepG2	liver:	n/a	chr11:57270492-57270507
38	MAZ	chr11:57270379-57270625	HepG2	liver:	n/a	n/a
39	CTCF	chr11:57270360-57270510	Caco-2	colon:	n/a	n/a
40	FOXA1	chr11:57270392-57270724	A549	lung:	n/a	n/a
41	NR3C1	chr11:57270434-57270717	A549	lung:	n/a	chr11:57270555-57270569 chr11:57270549-57270575
42	FOXA1	chr11:57270222-57270825	HepG2	liver:	n/a	n/a
43	FOXA2	chr11:57270383-57270722	A549	lung:	n/a	n/a
44	NR2F2	chr11:57270164-57270894	HepG2	liver:	n/a	chr11:57270492-57270507
45	FOXA1	chr11:57270238-57270738	HepG2	liver:	n/a	n/a
46	NR3C1	chr11:57270415-57270701	A549	lung:	n/a	chr11:57270555-57270569 chr11:57270549-57270575
47	FOXA1	chr11:57270366-57270717	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57262197..57265098-chr11:57268872..57270769,2	K562	blood:
2	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1001956	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2250673	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258835	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2467327	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2509899	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511984	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511986	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2581921	0.83[ASN][1000 genomes]
rs2581922	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581923	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2584856	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2584862	0.90[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729353	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729363	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2729371	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2729377	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2729384	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729387	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729394	0.82[ASN][1000 genomes]
rs2848626	0.90[ASN][1000 genomes]
rs2848634	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848635	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2848640	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851117	0.86[CEU][hapmap];0.91[TSI][hapmap]

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:25)

SNP	Gene	Cis/trans	Tissue	Source
rs2649667	SLC43A1	cis	cerebellum	SCAN
rs2649667	SLC43A1	cis	parietal	SCAN
rs2649667	TIMM10	trans	brain	seeQTL
rs2649667	TIMM10	cis	Esophagus Muscularis	GTEx
rs2649667	TIMM10	cis	Frontal Cortex	GTEx
rs2649667	TIMM10	cis	multi-tissue	Pritchard
rs2649667	OR5AP2	cis	parietal	SCAN
rs2649667	TIMM10	cis	Temporal Cortex	GTEx
rs2649667	TIMM10	cis	Artery Tibial	GTEx
rs2649667	TIMM10	cis	cerebellum	SCAN
rs2649667	TIMM10	cis	Cerebellum	GTEx
rs2649667	TIMM10	cis	Brain Pons	GTEx
rs2649667	CMPK1	trans	parietal	SCAN
rs2649667	TIMM10	cis	parietal	SCAN
rs2649667	TIMM10	cis	brain	seeQTL
rs2649667	TIMM10	cis	lesional skin	skin_eQTL
rs2649667	TIMM10	cis	Esophagus Mucosa	GTEx
rs2649667	TIMM10	cis	Muscle Skeletal	GTEx
rs2649667	OR10Q1	cis	parietal	SCAN
rs2649667	TIMM10	cis	lymphoblastoid	seeQTL
rs2649667	TIMM10	cis	Thyroid	GTEx
rs2649667	TIMM10	cis	Lymphoblastoid	GTEx
rs2649667	TIMM10	cis	Artery Aorta	GTEx
rs2649667	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx
rs2649667	TIMM10	cis	Heart Left Ventricle	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
8	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
11	chr11:57261400-57281400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:57261800-57279600	Weak transcription	Dnd41	blood
13	chr11:57267200-57279400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr11:57267600-57270800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr11:57267600-57274600	Genic enhancers	HepG2	liver
16	chr11:57267600-57280200	Weak transcription	Primary B cells from cord blood	blood
17	chr11:57267600-57281200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr11:57267600-57281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:57267800-57270600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr11:57267800-57270600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:57267800-57270600	Weak transcription	Fetal Intestine Large	intestine
22	chr11:57267800-57273600	Weak transcription	Osteobl	bone
23	chr11:57267800-57274000	Weak transcription	HSMM	muscle
24	chr11:57267800-57280600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:57267800-57281400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:57267800-57281400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:57267800-57281400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:57267800-57281600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:57267800-57281600	Weak transcription	NH-A	brain
30	chr11:57267800-57281800	Weak transcription	Aorta	Aorta
31	chr11:57268000-57276400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:57268000-57276600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:57268000-57279600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:57268000-57281000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:57268000-57281800	Weak transcription	Small Intestine	intestine
36	chr11:57268200-57271800	Strong transcription	Fetal Stomach	stomach
37	chr11:57268200-57280000	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:57268200-57280400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:57268200-57280800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:57268200-57281600	Weak transcription	Brain Angular Gyrus	brain
41	chr11:57268400-57271800	Weak transcription	K562	blood
42	chr11:57268400-57281800	Weak transcription	Fetal Lung	lung
43	chr11:57268600-57271800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:57268600-57280400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:57268600-57280800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:57268600-57280800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:57268600-57281800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:57268800-57280200	Weak transcription	NHLF	lung
49	chr11:57268800-57281200	Weak transcription	Lung	lung
50	chr11:57268800-57281600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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