Variant report

Variant	rs2584856
Chromosome Location	chr11:57267312-57267313
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	POLR2A	chr11:57266940-57267540	Hela-S3	cervix:	n/a	n/a
2	GATA1	chr11:57266850-57267627	PBDE	blood:	n/a	n/a
3	POLR2A	chr11:57266926-57267347	SK-N-SH	brain:	n/a	n/a
4	TBP	chr11:57266947-57267561	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZBTB7A	chr11:57267178-57267604	ECC-1	luminal epithelium:	n/a	n/a
6	NR2F2	chr11:57266767-57267691	K562	blood:	n/a	n/a
7	ZBTB7A	chr11:57267188-57267444	HepG2	liver:	n/a	n/a
8	ZNF143	chr11:57267174-57267492	Hela-S3	cervix:	n/a	n/a
9	NFYB	chr11:57267042-57267449	Hela-S3	cervix:	n/a	chr11:57267217-57267231
10	ARID3A	chr11:57267246-57267438	K562	blood:	n/a	n/a
11	POLR2A	chr11:57266900-57267423	K562	blood:	n/a	n/a
12	SIN3A	chr11:57267014-57267774	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr11:57266986-57267401	A549	lung:	n/a	n/a
14	CTCF	chr11:57267220-57267370	HCPEpiC	choroid plexus:	n/a	n/a
15	BRCA1	chr11:57267144-57267497	Hela-S3	cervix:	n/a	n/a
16	MAX	chr11:57266824-57267332	A549	lung:	n/a	chr11:57267174-57267184
17	POLR2A	chr11:57266744-57267645	HUVEC	blood vessel:	n/a	n/a
18	RFX5	chr11:57267274-57267344	K562	blood:	n/a	n/a
19	ELK1	chr11:57267306-57267312	K562	blood:	n/a	n/a
20	POLR2A	chr11:57266921-57267395	HUVEC	blood vessel:	n/a	n/a
21	MAZ	chr11:57266716-57268117	IMR90	lung:	n/a	chr11:57267174-57267184
22	POLR2A	chr11:57266859-57267346	HUVEC	blood vessel:	n/a	n/a
23	RAD21	chr11:57267185-57267366	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr11:57266919-57267713	HepG2	liver:	n/a	n/a
25	HDAC2	chr11:57267068-57267407	K562	blood:	n/a	n/a
26	TCF7L2	chr11:57267293-57267903	Hela-S3	cervix:	n/a	n/a
27	SP4	chr11:57267006-57267522	H1-hESC	embryonic stem cell:	n/a	chr11:57267154-57267170 chr11:57267238-57267249 chr11:57267152-57267168
28	POLR2A	chr11:57266844-57267411	U87	brain:	n/a	n/a
29	POLR2A	chr11:57266909-57268151	HepG2	liver:	n/a	n/a
30	NR2F2	chr11:57267085-57267803	K562	blood:	n/a	n/a
31	TBP	chr11:57267011-57267717	K562	blood:	n/a	n/a
32	POLR2A	chr11:57267237-57267410	H1-hESC	embryonic stem cell:	n/a	n/a
33	NRF1	chr11:57267248-57267498	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXA1	chr11:57267173-57267753	HepG2	liver:	n/a	chr11:57267601-57267613
35	MAX	chr11:57266763-57267913	A549	lung:	n/a	chr11:57267174-57267184
36	CTCF	chr11:57267200-57267350	AG04449	skin:	n/a	n/a
37	POLR2A	chr11:57266892-57267433	H1-hESC	embryonic stem cell:	n/a	n/a
38	ELK1	chr11:57266936-57267577	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr11:57266841-57267494	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr11:57267190-57267321	Kidney_OC	kidney:	n/a	n/a
41	NFYA	chr11:57267075-57267443	Hela-S3	cervix:	n/a	chr11:57267217-57267231
42	HEY1	chr11:57266926-57267536	HepG2	liver:	n/a	n/a
43	MAZ	chr11:57266983-57267626	HepG2	liver:	n/a	chr11:57267174-57267184
44	POLR2A	chr11:57266811-57267647	PFSK-1	brain:	n/a	n/a
45	CTCF	chr11:57267260-57267410	SK-N-SH_RA	brain:	n/a	n/a
46	NFYA	chr11:57267052-57267440	K562	blood:	n/a	chr11:57267217-57267231
47	RCOR1	chr11:57266938-57267443	Hela-S3	cervix:	n/a	n/a
48	UBTF	chr11:57267276-57267537	K562	blood:	n/a	n/a
49	CCNT2	chr11:57266930-57267453	K562	blood:	n/a	chr11:57267157-57267166 chr11:57266982-57266991 chr11:57267376-57267385
50	NR3C1	chr11:57266819-57267372	A549	lung:	n/a	chr11:57267180-57267193

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	chr11:57227341..57230250-chr11:57267205..57269644,2	K562	blood:
4	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:
5	chr11:57265680..57269520-chr11:57278275..57283954,6	K562	blood:

Variant related genes	Relation type
SLC43A1	TF binding region
ENSG00000186907	Chromatin interaction
ENSG00000149150	Chromatin interaction
ENSG00000255301	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs1001956	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10750864	0.81[AMR][1000 genomes]
rs2250673	0.85[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	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2509899	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511984	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2511986	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2581921	0.81[ASN][1000 genomes]
rs2581922	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]
rs2581923	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2584862	0.95[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2649667	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]
rs2729353	1.00[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729363	1.00[JPT][hapmap]
rs2729377	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848635	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2848640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851117	0.90[CEU][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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2584856	TIMM10	cis	Temporal Cortex	GTEx
rs2584856	TIMM10	cis	Thyroid	GTEx
rs2584856	TIMM10	cis	Esophagus Muscularis	GTEx
rs2584856	TIMM10	cis	lesional skin	skin_eQTL
rs2584856	TIMM10	cis	Brain Pons	GTEx
rs2584856	TIMM10	cis	Artery Aorta	GTEx
rs2584856	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2584856	TIMM10	cis	Esophagus Mucosa	GTEx
rs2584856	TIMM10	cis	Frontal Cortex	GTEx
rs2584856	TIMM10	cis	Cerebellum	GTEx
rs2584856	TIMM10	cis	Artery Tibial	GTEx
rs2584856	TIMM10	cis	Heart Left Ventricle	GTEx
rs2584856	TIMM10	cis	multi-tissue	Pritchard
rs2584856	TIMM10	cis	Lymphoblastoid	GTEx
rs2584856	TIMM10	cis	Muscle Skeletal	GTEx
rs2584856	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57251000-57267400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:57251200-57280600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:57251400-57279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:57251400-57281200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:57252600-57267600	Weak transcription	Small Intestine	intestine
6	chr11:57253800-57276400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:57253800-57279000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:57255200-57269600	Weak transcription	Esophagus	oesophagus
9	chr11:57256400-57273000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:57257000-57267800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr11:57257400-57281400	Weak transcription	Primary T cells from cord blood	blood
12	chr11:57258800-57279200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:57259000-57267800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
16	chr11:57261400-57281400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:57261800-57279600	Weak transcription	Dnd41	blood
18	chr11:57263000-57270000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:57264800-57269800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr11:57265400-57267800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:57266000-57267400	Enhancers	Fetal Heart	heart
22	chr11:57266000-57267800	Enhancers	Lung	lung
23	chr11:57266000-57268000	Enhancers	Gastric	stomach
24	chr11:57266000-57270000	Enhancers	Right Atrium	heart
25	chr11:57266200-57267400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr11:57266200-57267600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr11:57266600-57268000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr11:57266800-57267400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:57266800-57267400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:57266800-57267400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr11:57266800-57267400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:57266800-57267400	Active TSS	Brain Anterior Caudate	brain
33	chr11:57266800-57267400	Active TSS	Brain Substantia Nigra	brain
34	chr11:57266800-57267400	Enhancers	Fetal Brain Male	brain
35	chr11:57266800-57267400	Enhancers	Thymus	Thymus
36	chr11:57266800-57267400	Active TSS	NH-A	brain
37	chr11:57266800-57267600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:57266800-57267600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:57266800-57267600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:57266800-57267600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr11:57266800-57267600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:57266800-57267600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:57266800-57267600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:57266800-57267600	Active TSS	Brain Germinal Matrix	brain
45	chr11:57266800-57267600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr11:57266800-57267600	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr11:57266800-57267600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
48	chr11:57266800-57267600	Active TSS	Fetal Kidney	kidney
49	chr11:57266800-57267600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr11:57266800-57267600	Flanking Active TSS	Fetal Muscle Trunk	muscle

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