Variant report

Variant	rs10840106
Chromosome Location	chr11:8701836-8701837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:8701787-8702633	HCT-116	colon:	n/a	n/a
2	POLR2A	chr11:8701609-8702121	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr11:8701791-8701943	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:8700198-8712489	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr11:8700848-8711808	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:8701551-8701986	HCT-116	colon:	n/a	n/a
7	POLR2A	chr11:8700610-8712688	K562	blood:	n/a	n/a
8	POLR2A	chr11:8700905-8702664	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:8701773..8703653-chr11:8846645..8848951,2	MCF-7	breast:
2	chr11:8701660..8705909-chr11:8738922..8746228,9	MCF-7	breast:
3	chr11:8674451..8677275-chr11:8701396..8703424,3	K562	blood:
4	chr11:8701763..8703828-chr11:8934006..8936271,2	K562	blood:
5	chr11:8701282..8703151-chr11:8791566..8793541,2	K562	blood:
6	chr11:8675317..8677275-chr11:8701534..8703424,2	K562	blood:
7	chr11:8699371..8704185-chr11:8984475..8986762,4	K562	blood:
8	chr11:8701293..8704221-chr11:8890079..8892942,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNORA3	TF binding region
RPL27A	TF binding region
ENSG00000166444	Chromatin interaction
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10840105	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042041	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036422	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073684	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35104495	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59942149	0.80[AFR][1000 genomes]
rs7123653	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7940366	0.89[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs10840106	ST5	cis	cerebellum	SCAN
rs10840106	TRIM66	cis	Liver	GTEx
rs10840106	RPL27A	cis	cerebellum	SCAN
rs10840106	ST5	cis	parietal	SCAN
rs10840106	TRIM66	cis	Esophagus Muscularis	GTEx
rs10840106	TRIM66	cis	Adipose Subcutaneous	GTEx
rs10840106	TRIM66	cis	lung	GTEx
rs10840106	ASCL3	cis	parietal	SCAN
rs10840106	TRIM66	cis	Artery Tibial	GTEx
rs10840106	NRIP3	cis	cerebellum	SCAN
rs10840106	TRIM66	cis	Thyroid	GTEx
rs10840106	RPL27A	cis	parietal	SCAN
rs10840106	OR52A1	cis	parietal	SCAN
rs10840106	TRIM66	cis	parietal	SCAN
rs10840106	TRIM66	cis	Heart Left Ventricle	GTEx
rs10840106	TRIM66	cis	Lymphoblastoid	GTEx
rs10840106	STK33	cis	cerebellum	SCAN
rs10840106	AK000908	cis	multi-tissue	Pritchard
rs10840106	ADM	cis	cerebellum	SCAN
rs10840106	HSS00146441	cis	multi-tissue	Pritchard
rs10840106	LOC256273	cis	multi-tissue	Pritchard
rs10840106	SNORA45	cis	cerebellum	SCAN
rs10840106	TRIM66	cis	Esophagus Mucosa	GTEx
rs10840106	TRIM66	cis	Whole Blood	GTEx
rs10840106	TRIM66	cis	Nerve Tibial	GTEx
rs10840106	LOC256273	cis	normal skin	skin_eQTL
rs10840106	TRIM66	cis	Skin Sun Exposed Lower leg	GTEx
rs10840106		cis	Lymphoblastoid	GTEx
rs10840106	TRIM66	cis	Muscle Skeletal	GTEx
rs10840106	SNORA45	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
2	chr11:8690000-8703000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:8693600-8703000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:8693600-8703200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:8693600-8703200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:8693600-8703200	Weak transcription	Fetal Lung	lung
7	chr11:8693600-8703400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:8693600-8703400	Weak transcription	Ovary	ovary
9	chr11:8693800-8703000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:8693800-8703000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:8693800-8703000	Weak transcription	Hela-S3	cervix
12	chr11:8693800-8703200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:8693800-8703200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:8693800-8703200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:8693800-8703200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:8693800-8703200	Weak transcription	Brain Substantia Nigra	brain
17	chr11:8693800-8703200	Weak transcription	Colonic Mucosa	Colon
18	chr11:8693800-8703200	Weak transcription	Fetal Brain Female	brain
19	chr11:8693800-8703400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:8693800-8703400	Weak transcription	Brain Germinal Matrix	brain
21	chr11:8693800-8703600	Weak transcription	Spleen	Spleen
22	chr11:8694000-8702200	Weak transcription	HSMM	muscle
23	chr11:8694000-8702200	Weak transcription	K562	blood
24	chr11:8694000-8703000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:8694000-8703000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:8694000-8703000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:8694000-8703000	Weak transcription	Fetal Muscle Leg	muscle
28	chr11:8694000-8703200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:8694000-8703200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:8694000-8703200	Weak transcription	Brain Hippocampus Middle	brain
31	chr11:8694000-8703200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:8694000-8703200	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:8694000-8703200	Weak transcription	Fetal Brain Male	brain
34	chr11:8694000-8703200	Weak transcription	Fetal Kidney	kidney
35	chr11:8694000-8703200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:8694000-8703200	Weak transcription	Thymus	Thymus
37	chr11:8694000-8703200	Weak transcription	NH-A	brain
38	chr11:8694000-8703200	Weak transcription	Osteobl	bone
39	chr11:8694000-8703400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:8694000-8703400	Weak transcription	Esophagus	oesophagus
41	chr11:8694000-8703400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr11:8694200-8703000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:8694200-8703000	Weak transcription	HUVEC	blood vessel
44	chr11:8694200-8703200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:8694200-8703200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr11:8694200-8703200	Weak transcription	HMEC	breast
47	chr11:8694200-8703200	Weak transcription	HSMMtube	muscle
48	chr11:8694200-8703400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:8694400-8703400	Weak transcription	Left Ventricle	heart
50	chr11:8695600-8703200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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