Variant report

Variant	rs11639821
Chromosome Location	chr16:12092575-12092576
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	EBF1	chr16:12092573-12092928	GM12878	blood:	n/a	chr16:12092790-12092801
2	SPI1	chr16:12092466-12092648	GM12891	blood:	n/a	chr16:12092576-12092589
3	SPI1	chr16:12092482-12092655	K562	blood:	n/a	chr16:12092576-12092589

Variant related genes	Relation type
SNX29	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10163386	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11075041	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11641950	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11644227	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11648938	0.83[MEX][hapmap]
rs11859213	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11862467	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13334063	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2865105	0.93[CEU][hapmap]
rs3844112	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3916255	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417938	0.91[MEX][hapmap]
rs436838	0.82[MEX][hapmap]
rs442234	0.91[MEX][hapmap]
rs59446863	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6498260	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6498261	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6498262	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7197059	0.89[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7206768	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8044943	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8045634	0.81[MEX][hapmap]
rs8050827	0.81[MEX][hapmap]
rs8051012	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8060439	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8062691	0.87[MEX][hapmap]
rs9929844	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11639821	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs11639821	GSPT1	cis	parietal	SCAN
rs11639821	TNFRSF17	cis	parietal	SCAN
rs11639821	RP11-166B2.1	cis	Whole Blood	GTEx
rs11639821	TNFRSF17	cis	cerebellum	SCAN
rs11639821	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12072000-12093600	Weak transcription	Fetal Stomach	stomach
4	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
5	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr16:12072400-12096400	Weak transcription	Ovary	ovary
8	chr16:12072400-12104400	Weak transcription	NHLF	lung
9	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr16:12079600-12109600	Weak transcription	Gastric	stomach
14	chr16:12080200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:12082000-12093000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:12083400-12102800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
18	chr16:12086800-12096600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr16:12087400-12092800	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr16:12088200-12100800	Weak transcription	Fetal Brain Female	brain
21	chr16:12088600-12093800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr16:12088600-12098200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr16:12088600-12104200	Weak transcription	Right Ventricle	heart
24	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
25	chr16:12088600-12110000	Weak transcription	NH-A	brain
26	chr16:12088800-12094400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr16:12088800-12096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr16:12088800-12096400	Weak transcription	Right Atrium	heart
29	chr16:12088800-12098600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:12088800-12106600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:12088800-12108200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr16:12088800-12115400	Weak transcription	Placenta	Placenta
33	chr16:12089000-12093200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:12089000-12093800	Weak transcription	Brain Anterior Caudate	brain
35	chr16:12089000-12093800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr16:12089000-12093800	Weak transcription	Lung	lung
37	chr16:12089000-12094000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr16:12089000-12094400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr16:12089000-12094400	Weak transcription	Left Ventricle	heart
40	chr16:12089000-12094600	Weak transcription	Brain Angular Gyrus	brain
41	chr16:12089000-12099800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr16:12089000-12104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr16:12089400-12093400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr16:12089400-12103000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr16:12090200-12092600	Weak transcription	Brain Hippocampus Middle	brain
46	chr16:12090200-12094200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr16:12090600-12093200	Weak transcription	Adipose Nuclei	Adipose
48	chr16:12090800-12093800	Weak transcription	Aorta	Aorta
49	chr16:12090800-12093800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr16:12090800-12096400	Weak transcription	Primary hematopoietic stem cells	blood

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