Variant report

Variant	rs2581922
Chromosome Location	chr11:57265400-57265401
allele	C/T
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	MAZ	chr11:57265211-57265588	HepG2	liver:	n/a	n/a
2	MAFF	chr11:57265089-57265511	HepG2	liver:	n/a	n/a
3	YY1	chr11:57265163-57265483	HepG2	liver:	n/a	n/a
4	MYC	chr11:57265111-57265723	HepG2	liver:	n/a	n/a
5	JUND	chr11:57265223-57265568	HepG2	liver:	n/a	n/a
6	RAD21	chr11:57265208-57265558	HepG2	liver:	n/a	n/a
7	HEY1	chr11:57265116-57265524	HepG2	liver:	n/a	n/a
8	NR2F2	chr11:57264667-57265796	HepG2	liver:	n/a	n/a
9	MAFK	chr11:57264918-57265497	HepG2	liver:	n/a	n/a
10	MAX	chr11:57264433-57265791	HepG2	liver:	n/a	n/a
11	RXRA	chr11:57264942-57265801	HepG2	liver:	n/a	chr11:57265358-57265372
12	RAD21	chr11:57265275-57265618	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:57264832-57266376	HepG2	liver:	n/a	n/a
14	MYBL2	chr11:57264528-57265774	HepG2	liver:	n/a	n/a
15	TEAD4	chr11:57265228-57265558	HepG2	liver:	n/a	n/a
16	RXRA	chr11:57265130-57265688	HepG2	liver:	n/a	chr11:57265358-57265372
17	EP300	chr11:57265136-57265684	HepG2	liver:	n/a	n/a
18	MAFK	chr11:57265256-57265591	HepG2	liver:	n/a	n/a
19	HNF4A	chr11:57265209-57265689	HepG2	liver:	n/a	chr11:57265358-57265371 chr11:57265358-57265371 chr11:57265357-57265370 chr11:57265357-57265369 chr11:57265459-57265474 chr11:57265355-57265373 chr11:57265358-57265370 chr11:57265358-57265370
20	ZBTB7A	chr11:57265255-57265558	HepG2	liver:	n/a	n/a
21	FOXA1	chr11:57265183-57265764	HepG2	liver:	n/a	chr11:57265431-57265443
22	HEY1	chr11:57265200-57265620	HepG2	liver:	n/a	n/a
23	MBD4	chr11:57264737-57265680	HepG2	liver:	n/a	n/a
24	FOXA1	chr11:57265127-57265793	HepG2	liver:	n/a	chr11:57265431-57265443
25	FOXA2	chr11:57264922-57265936	HepG2	liver:	n/a	chr11:57265431-57265443
26	FOXA2	chr11:57265173-57265687	HepG2	liver:	n/a	chr11:57265431-57265443
27	FOXA1	chr11:57265144-57265719	HepG2	liver:	n/a	chr11:57265431-57265443
28	NFIC	chr11:57265167-57265675	HepG2	liver:	n/a	n/a
29	REST	chr11:57265217-57265608	HepG2	liver:	n/a	n/a
30	EP300	chr11:57264573-57265778	HepG2	liver:	n/a	n/a
31	CHD2	chr11:57265274-57265534	HepG2	liver:	n/a	n/a
32	USF2	chr11:57264832-57265400	HepG2	liver:	n/a	n/a
33	MAX	chr11:57264634-57265485	HepG2	liver:	n/a	n/a
34	FOSL2	chr11:57265069-57265632	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:57264664-57265620	HepG2	liver:	n/a	n/a
36	RFX5	chr11:57264863-57265698	HepG2	liver:	n/a	n/a
37	SMC3	chr11:57264887-57265629	HepG2	liver:	n/a	n/a
38	MAX	chr11:57264437-57265774	HepG2	liver:	n/a	n/a
39	TBP	chr11:57264899-57265763	HepG2	liver:	n/a	n/a
40	CEBPB	chr11:57265225-57265758	HepG2	liver:	n/a	n/a
41	RAD21	chr11:57265265-57265570	HepG2	liver:	n/a	n/a
42	POLR2A	chr11:57264904-57267010	K562	blood:	n/a	n/a
43	HDAC2	chr11:57265113-57265790	HepG2	liver:	n/a	n/a
44	POLR2A	chr11:57265347-57265508	H1-hESC	embryonic stem cell:	n/a	n/a
45	CEBPD	chr11:57265182-57265567	HepG2	liver:	n/a	n/a
46	CEBPB	chr11:57265345-57265675	HepG2	liver:	n/a	n/a
47	FOXA1	chr11:57264681-57265781	HepG2	liver:	n/a	chr11:57265431-57265443
48	ARID3A	chr11:57264661-57265721	HepG2	liver:	n/a	n/a
49	SP1	chr11:57264549-57265780	HepG2	liver:	n/a	n/a
50	HNF4A	chr11:57265102-57265676	HepG2	liver:	n/a	chr11:57265358-57265371 chr11:57265358-57265371 chr11:57265357-57265370 chr11:57265357-57265369 chr11:57265459-57265474 chr11:57265355-57265373 chr11:57265358-57265370 chr11:57265358-57265370

No.	Distal block	Cell Line	Cell type
1	chr11:57260621..57264536-chr11:57264640..57268839,7	K562	blood:
2	chr11:57243749..57245778-chr11:57264332..57267920,3	MCF-7	breast:
3	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000149150	Chromatin interaction
ENSG00000255301	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1001956	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750864	0.81[AMR][1000 genomes]
rs2250673	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2258835	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2467327	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2509899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511984	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2511986	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2581921	0.81[ASN][1000 genomes]
rs2581923	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2584856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2584862	0.95[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2649667	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]
rs2729353	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729363	1.00[JPT][hapmap]
rs2729371	0.81[TSI][hapmap]
rs2729377	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729387	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729394	0.80[ASN][1000 genomes]
rs2848626	0.89[ASN][1000 genomes]
rs2848634	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848635	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2848640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851117	0.90[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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2581922	TIMM10	cis	Artery Aorta	GTEx
rs2581922	TIMM10	cis	Thyroid	GTEx
rs2581922	TIMM10	cis	Temporal Cortex	GTEx
rs2581922	TIMM10	cis	cerebellum	SCAN
rs2581922	SLC43A1	cis	cerebellum	SCAN
rs2581922	SLC43A1	cis	parietal	SCAN
rs2581922	TIMM10	cis	Artery Tibial	GTEx
rs2581922	OR5AP2	cis	parietal	SCAN
rs2581922	OR10Q1	cis	parietal	SCAN
rs2581922	SLC43A3	cis	cerebellum	SCAN
rs2581922	TIMM10	cis	Esophagus Muscularis	GTEx
rs2581922	TIMM10	cis	Muscle Skeletal	GTEx
rs2581922	TIMM10	cis	Frontal Cortex	GTEx
rs2581922	TIMM10	cis	parietal	SCAN
rs2581922	CMPK1	trans	parietal	SCAN
rs2581922	TIMM10	cis	Cerebellum	GTEx
rs2581922	TIMM10	cis	Esophagus Mucosa	GTEx
rs2581922	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx
rs2581922	TIMM10	cis	Heart Left Ventricle	GTEx
rs2581922	TIMM10	cis	multi-tissue	Pritchard
rs2581922	TIMM10	cis	Brain Pons	GTEx
rs2581922	TIMM10	cis	lymphoblastoid	seeQTL
rs2581922	TIMM10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57250800-57266000	Weak transcription	Right Atrium	heart
2	chr11:57251000-57266800	Weak transcription	HUVEC	blood vessel
3	chr11:57251000-57267400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:57251200-57266800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:57251200-57266800	Weak transcription	HSMM	muscle
6	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:57251400-57266000	Weak transcription	Brain Substantia Nigra	brain
8	chr11:57251400-57266200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:57251400-57266400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:57251400-57266800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:57251600-57266800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:57251800-57266200	Strong transcription	Fetal Stomach	stomach
15	chr11:57252600-57267600	Weak transcription	Small Intestine	intestine
16	chr11:57252800-57266800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:57253200-57266800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr11:57253200-57266800	Weak transcription	Thymus	Thymus
19	chr11:57253400-57266800	Weak transcription	Fetal Thymus	thymus
20	chr11:57253800-57266800	Weak transcription	Colonic Mucosa	Colon
21	chr11:57253800-57266800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:57253800-57266800	Weak transcription	Osteobl	bone
23	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:57255200-57266800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:57255200-57269600	Weak transcription	Esophagus	oesophagus
27	chr11:57256000-57266800	Weak transcription	HSMMtube	muscle
28	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:57256800-57266800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:57257000-57267800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr11:57257200-57266600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
33	chr11:57258000-57266800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:57258600-57266800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr11:57258800-57266800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:57258800-57266800	Weak transcription	NHDF-Ad	bronchial
37	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:57259000-57267800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:57259200-57266200	Weak transcription	Left Ventricle	heart
40	chr11:57259200-57266400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr11:57259200-57266800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:57259200-57267200	Weak transcription	Aorta	Aorta
43	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
45	chr11:57259400-57266000	Weak transcription	Right Ventricle	heart
46	chr11:57259600-57266000	Weak transcription	Spleen	Spleen
47	chr11:57260600-57266600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:57260600-57266800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:57261000-57266800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:57261200-57266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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