Variant report

Variant	rs1001956
Chromosome Location	chr11:57266949-57266950
allele	C/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	chr11:57266940-57267540	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	POLR2A	chr11:57266942-57267159	H1-hESC	embryonic stem cell:	n/a	n/a
6	NR2F2	chr11:57266767-57267691	K562	blood:	n/a	n/a
7	POLR2A	chr11:57266900-57267423	K562	blood:	n/a	n/a
8	MAX	chr11:57266824-57267332	A549	lung:	n/a	chr11:57267174-57267184
9	POLR2A	chr11:57266744-57267645	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr11:57266921-57267395	HUVEC	blood vessel:	n/a	n/a
11	MAZ	chr11:57266716-57268117	IMR90	lung:	n/a	chr11:57267174-57267184
12	POLR2A	chr11:57266859-57267346	HUVEC	blood vessel:	n/a	n/a
13	MXI1	chr11:57266919-57267713	HepG2	liver:	n/a	n/a
14	CEBPD	chr11:57266939-57267299	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:57266844-57267411	U87	brain:	n/a	n/a
16	NR3C1	chr11:57266927-57267232	A549	lung:	n/a	chr11:57267180-57267193
17	POLR2A	chr11:57266901-57267286	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:57266909-57268151	HepG2	liver:	n/a	n/a
19	MAX	chr11:57266763-57267913	A549	lung:	n/a	chr11:57267174-57267184
20	POLR2A	chr11:57266892-57267433	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELK1	chr11:57266936-57267577	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr11:57266841-57267494	ECC-1	luminal epithelium:	n/a	n/a
23	HEY1	chr11:57266926-57267536	HepG2	liver:	n/a	n/a
24	POLR2A	chr11:57266811-57267647	PFSK-1	brain:	n/a	n/a
25	RCOR1	chr11:57266938-57267443	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr11:57266912-57267180	H1-hESC	embryonic stem cell:	n/a	n/a
27	CCNT2	chr11:57266930-57267453	K562	blood:	n/a	chr11:57267157-57267166 chr11:57266982-57266991 chr11:57267376-57267385
28	NR3C1	chr11:57266819-57267372	A549	lung:	n/a	chr11:57267180-57267193
29	TAF1	chr11:57266921-57267550	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr11:57266882-57267380	A549	lung:	n/a	n/a
31	GABPA	chr11:57266811-57267388	K562	blood:	n/a	chr11:57267157-57267166
32	SP1	chr11:57266896-57267616	H1-hESC	embryonic stem cell:	n/a	chr11:57267157-57267167 chr11:57266980-57266992 chr11:57266967-57266981 chr11:57267375-57267387 chr11:57267240-57267249 chr11:57267158-57267167 chr11:57267372-57267386 chr11:57267156-57267168 chr11:57267156-57267168 chr11:57267193-57267205 chr11:57267377-57267386 chr11:57266982-57266991 chr11:57267376-57267385 chr11:57267158-57267167 chr11:57267239-57267248 chr11:57267157-57267166 chr11:57266980-57266992 chr11:57267238-57267249 chr11:57267157-57267167 chr11:57267377-57267386 chr11:57267153-57267167
33	HEY1	chr11:57266938-57267224	HepG2	liver:	n/a	n/a
34	HMGN3	chr11:57266901-57267406	K562	blood:	n/a	n/a
35	TAF1	chr11:57266938-57267522	H1-hESC	embryonic stem cell:	n/a	n/a
36	NFIC	chr11:57266814-57267723	ECC-1	luminal epithelium:	n/a	n/a
37	NFIC	chr11:57266760-57267760	ECC-1	luminal epithelium:	n/a	n/a
38	SMC3	chr11:57266890-57267493	Hela-S3	cervix:	n/a	chr11:57267154-57267164
39	POLR2A	chr11:57266621-57267470	PFSK-1	brain:	n/a	n/a
40	NR3C1	chr11:57266839-57267424	A549	lung:	n/a	chr11:57267180-57267193
41	POLR2A	chr11:57264904-57267010	K562	blood:	n/a	n/a
42	FOXP2	chr11:57266875-57267405	PFSK-1	brain:	n/a	n/a
43	RFX5	chr11:57266935-57267562	Hela-S3	cervix:	n/a	chr11:57267082-57267090
44	POLR2A	chr11:57266865-57267391	A549	lung:	n/a	n/a
45	MAX	chr11:57266879-57267371	SK-N-SH	brain:	n/a	chr11:57267174-57267184
46	POLR2A	chr11:57266878-57267307	HepG2	liver:	n/a	n/a
47	BHLHE40	chr11:57266908-57267189	HepG2	liver:	n/a	n/a
48	POLR2A	chr11:57266926-57267459	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr11:57266656-57267733	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr11:57266935-57267871	Hela-S3	cervix:	n/a	chr11:57267174-57267184

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:
4	chr11:57265680..57269520-chr11:57278275..57283954,6	K562	blood:

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

Extended variants
information (count: 26 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2250673	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2258835	0.90[CEU][hapmap];1.00[JPT][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	0.94[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	0.85[CEU][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2581921	0.81[ASN][1000 genomes]
rs2581922	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]
rs2581923	0.95[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2584856	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]
rs2584862	0.90[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2649667	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]
rs2729353	0.95[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729363	0.91[JPT][hapmap]
rs2729377	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729384	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729387	0.85[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	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2848635	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2848640	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851117	0.85[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1001956	TIMM10	cis	Temporal Cortex	GTEx
rs1001956	TIMM10	cis	Artery Aorta	GTEx
rs1001956	TIMM10	cis	Artery Tibial	GTEx
rs1001956	TIMM10	cis	Brain Pons	GTEx
rs1001956	TIMM10	cis	Thyroid	GTEx
rs1001956	TIMM10	cis	lesional skin	skin_eQTL
rs1001956	TIMM10	cis	Cerebellum	GTEx
rs1001956	TIMM10	cis	Heart Left Ventricle	GTEx
rs1001956	TIMM10	cis	Frontal Cortex	GTEx
rs1001956	TIMM10	cis	multi-tissue	Pritchard
rs1001956	TIMM10	cis	Esophagus Muscularis	GTEx
rs1001956	TIMM10	cis	Esophagus Mucosa	GTEx
rs1001956	TIMM10	cis	Muscle Skeletal	GTEx
rs1001956	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1001956	TIMM10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 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	chr11:57259200-57267200	Weak transcription	Aorta	Aorta
15	chr11:57259200-57279000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:57259200-57280800	Weak transcription	GM12878-XiMat	blood
17	chr11:57261400-57281400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:57261800-57279600	Weak transcription	Dnd41	blood
19	chr11:57262200-57267000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:57263000-57270000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:57263400-57267000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:57264000-57267200	Enhancers	Placenta	Placenta
23	chr11:57264000-57267200	Enhancers	Stomach Mucosa	stomach
24	chr11:57264800-57269800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:57265400-57267800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:57266000-57267400	Enhancers	Fetal Heart	heart
27	chr11:57266000-57267800	Enhancers	Lung	lung
28	chr11:57266000-57268000	Enhancers	Gastric	stomach
29	chr11:57266000-57270000	Enhancers	Right Atrium	heart
30	chr11:57266200-57267400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr11:57266200-57267600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr11:57266600-57268000	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr11:57266800-57267000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:57266800-57267000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr11:57266800-57267000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr11:57266800-57267000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr11:57266800-57267000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:57266800-57267000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:57266800-57267000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr11:57266800-57267000	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr11:57266800-57267000	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr11:57266800-57267000	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr11:57266800-57267000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr11:57266800-57267000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:57266800-57267000	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr11:57266800-57267000	Flanking Active TSS	Fetal Lung	lung
47	chr11:57266800-57267000	Flanking Active TSS	Left Ventricle	heart
48	chr11:57266800-57267000	Active TSS	Placenta Amnion	Placenta Amnion
49	chr11:57266800-57267000	Flanking Active TSS	Psoas Muscle	Psoas
50	chr11:57266800-57267000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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