Variant report

Variant	rs1106950
Chromosome Location	chr17:45281405-45281406
allele	G/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	RUNX3	chr17:45281343-45281955	GM12878	blood:	n/a	n/a
2	EBF1	chr17:45281210-45281758	GM12878	blood:	n/a	n/a
3	IRF3	chr17:45281382-45281425	GM12878	blood:	n/a	n/a
4	IKZF1	chr17:45281264-45283770	GM12878	blood:	n/a	n/a
5	RUNX3	chr17:45281174-45283374	GM12878	blood:	n/a	n/a
6	MTA3	chr17:45281021-45281815	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:45281376-45281551	GM12878	blood:	n/a	n/a
8	UBTF	chr17:45281344-45281654	K562	blood:	n/a	n/a
9	ZNF384	chr17:45281264-45283379	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:45281307-45283371	Raji	blood:	n/a	n/a
11	YY1	chr17:45281405-45281578	K562	blood:	n/a	n/a
12	EP300	chr17:45281387-45283365	GM12878	blood:	n/a	chr17:45282472-45282486 chr17:45282746-45282753 chr17:45282429-45282442
13	NFIC	chr17:45281291-45281933	GM12878	blood:	n/a	n/a
14	JUND	chr17:45281377-45281673	K562	blood:	n/a	chr17:45281498-45281506 chr17:45281494-45281505 chr17:45281499-45281506

No.	Distal block	Cell Line	Cell type
1	chr17:45236830..45238763-chr17:45281000..45283045,2	K562	blood:
2	chr17:45273712..45279094-chr17:45279285..45284499,7	K562	blood:
3	chr17:45265425..45269379-chr17:45279788..45284697,6	K562	blood:
4	chr17:45265176..45269287-chr17:45280012..45282931,4	K562	blood:
5	chr17:45281266..45284177-chr17:45290868..45295313,4	K562	blood:

Variant related genes	Relation type
MYL4	TF binding region
ENSG00000004897	Chromatin interaction
ENSG00000198336	Chromatin interaction
ENSG00000239291	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1476498	0.95[CEU][hapmap]
rs1634265	0.95[CEU][hapmap]
rs16941650	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1713493	0.95[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs8071243	0.95[CEU][hapmap]
rs858670	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs858677	0.95[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs858678	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs867859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs908359	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1106950	HSPB9	cis	cerebellum	SCAN
rs1106950	TUBG1	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45274800-45282200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr17:45278200-45282200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:45278200-45282200	Weak transcription	Colonic Mucosa	Colon
4	chr17:45278200-45282200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr17:45279000-45282000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr17:45279000-45282200	Weak transcription	Stomach Mucosa	stomach
7	chr17:45279200-45282000	Weak transcription	Fetal Intestine Small	intestine
8	chr17:45279200-45282000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:45279400-45282200	Weak transcription	Fetal Intestine Large	intestine
10	chr17:45280200-45282400	Enhancers	Primary B cells from peripheral blood	blood
11	chr17:45280400-45282200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:45280400-45282600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:45280600-45282800	Enhancers	Dnd41	blood
14	chr17:45280800-45282200	Enhancers	Primary B cells from cord blood	blood
15	chr17:45281000-45281600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr17:45281000-45281800	Enhancers	Duodenum Mucosa	Duodenum
17	chr17:45281000-45281800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr17:45281000-45282000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:45281000-45282200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr17:45281000-45282200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr17:45281000-45282200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr17:45281000-45282200	Enhancers	Adipose Nuclei	Adipose
23	chr17:45281000-45282200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr17:45281000-45282200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr17:45281000-45282200	Enhancers	HSMM	muscle
26	chr17:45281000-45282200	Enhancers	HSMMtube	muscle
27	chr17:45281000-45282200	Enhancers	NHDF-Ad	bronchial
28	chr17:45281000-45282200	Enhancers	Osteobl	bone
29	chr17:45281000-45282400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr17:45281000-45282400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:45281000-45282600	Enhancers	Primary T cells from cord blood	blood
32	chr17:45281000-45282600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr17:45281000-45282600	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr17:45281000-45283200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr17:45281000-45283200	Enhancers	Brain Substantia Nigra	brain
36	chr17:45281000-45283200	Enhancers	Small Intestine	intestine
37	chr17:45281000-45283400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:45281000-45283400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:45281000-45283400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:45281000-45283400	Enhancers	NH-A	brain
41	chr17:45281000-45283600	Enhancers	Primary hematopoietic stem cells	blood
42	chr17:45281000-45283600	Enhancers	Placenta	Placenta
43	chr17:45281000-45283600	Flanking Active TSS	GM12878-XiMat	blood
44	chr17:45281000-45283600	Enhancers	HMEC	breast
45	chr17:45281000-45283600	Enhancers	NHLF	lung
46	chr17:45281000-45283800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:45281000-45286000	Enhancers	Fetal Muscle Leg	muscle
48	chr17:45281000-45288400	Enhancers	Fetal Thymus	thymus
49	chr17:45281200-45281600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:45281200-45281600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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