Variant report

Variant	rs10840101
Chromosome Location	chr11:8671369-8671370
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	JUND	chr11:8670830-8671416	SK-N-SH	brain:	n/a	chr11:8671113-8671124 chr11:8671116-8671126 chr11:8671117-8671126 chr11:8671116-8671126 chr11:8671115-8671127 chr11:8671116-8671126 chr11:8671116-8671126
2	JUND	chr11:8670895-8671475	SK-N-SH	brain:	n/a	chr11:8671113-8671124 chr11:8671116-8671126 chr11:8671117-8671126 chr11:8671116-8671126 chr11:8671115-8671127 chr11:8671116-8671126 chr11:8671116-8671126
3	MAZ	chr11:8670875-8671741	IMR90	lung:	n/a	n/a
4	POLR2A	chr11:8663090-8674809	K562	blood:	n/a	n/a
5	POLR2A	chr11:8670886-8671499	U87	brain:	n/a	n/a
6	POLR2A	chr11:8670920-8671499	U87	brain:	n/a	n/a
7	FOSL2	chr11:8670814-8671416	SK-N-SH	brain:	n/a	chr11:8671113-8671124 chr11:8671116-8671126 chr11:8671117-8671126 chr11:8671116-8671126 chr11:8671115-8671127 chr11:8671116-8671126 chr11:8671116-8671126

No.	Distal block	Cell Line	Cell type
1	chr11:8670735..8672985-chr11:8708630..8710565,2	K562	blood:
2	chr11:8670015..8672581-chr11:8709209..8711726,2	MCF-7	breast:
3	chr11:8671281..8673032-chr11:8675425..8677604,2	K562	blood:

Variant related genes	Relation type
TRIM66	TF binding region
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10769917	0.83[AMR][1000 genomes]
rs10840098	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840103	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.96[ASN][1000 genomes]
rs11042032	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11605978	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs10840101	STK33	cis	cerebellum	SCAN
rs10840101	RPL27A	cis	parietal	SCAN
rs10840101	RPL27A	cis	cerebellum	SCAN
rs10840101	SNORA45	cis	cerebellum	SCAN
rs10840101	TRIM66	cis	lymphoblastoid	seeQTL
rs10840101	TRIM66	cis	Whole Blood	GTEx
rs10840101	TRIM22	cis	cerebellum	SCAN
rs10840101	ST5	cis	cerebellum	SCAN
rs10840101	NRIP3	cis	cerebellum	SCAN
rs10840101	OR52N1	cis	cerebellum	SCAN
rs10840101	OR52N5	cis	cerebellum	SCAN
rs10840101	SNORA45	cis	parietal	SCAN
rs10840101	TRIM66	cis	Muscle Skeletal	GTEx
rs10840101	TRIM66	cis	Heart Left Ventricle	GTEx
rs10840101	OR51V1	cis	cerebellum	SCAN
rs10840101	LOC256273	Cis_1M	lymphoblastoid	RTeQTL
rs10840101	TRIM66	Cis_1M	lymphoblastoid	RTeQTL
rs10840101	FLJ46111	cis	parietal	SCAN
rs10840101	TRIM66	cis	lung	GTEx
rs10840101	ASCL3	cis	parietal	SCAN

Chromatin state (count:118 , 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	chr11:8650800-8676200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:8652200-8675000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:8654000-8673800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr11:8654200-8673800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:8654200-8675600	Strong transcription	Stomach Smooth Muscle	stomach
7	chr11:8654400-8672400	Strong transcription	Brain Anterior Caudate	brain
8	chr11:8655000-8676400	Strong transcription	Primary T cells from cord blood	blood
9	chr11:8655200-8672600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:8655400-8673400	Strong transcription	Dnd41	blood
11	chr11:8656000-8672600	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:8656000-8672800	Strong transcription	Placenta	Placenta
13	chr11:8656600-8671600	Strong transcription	Brain Cingulate Gyrus	brain
14	chr11:8657200-8673800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:8657400-8672600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:8658000-8675200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:8658200-8672400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:8658200-8673800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:8658400-8671600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:8658600-8673000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:8658600-8674200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:8658600-8675000	Strong transcription	Liver	Liver
23	chr11:8659200-8673600	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:8661800-8673600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:8662600-8680200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:8662600-8692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:8662800-8675400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr11:8663000-8680200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:8663200-8680000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:8663600-8671400	Strong transcription	Fetal Intestine Large	intestine
31	chr11:8663600-8671600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:8663600-8676800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:8663800-8679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:8664200-8692800	Weak transcription	K562	blood
35	chr11:8664200-8700400	Weak transcription	Stomach Mucosa	stomach
36	chr11:8664400-8673600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:8664400-8679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:8664800-8679200	Weak transcription	Fetal Brain Male	brain
39	chr11:8664800-8679800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:8665800-8671800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr11:8665800-8692600	Weak transcription	Fetal Kidney	kidney
42	chr11:8666000-8672400	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:8666200-8671600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:8666200-8671600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:8666400-8672200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr11:8666400-8672600	Strong transcription	Thymus	Thymus
47	chr11:8666400-8673800	Strong transcription	Aorta	Aorta
48	chr11:8666400-8676000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:8666600-8671400	Strong transcription	Brain Substantia Nigra	brain
50	chr11:8666600-8671600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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