Variant report

Variant	rs436838
Chromosome Location	chr16:12073354-12073355
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	chr16:12073125-12073497	GM12878	blood:	n/a	n/a
2	ATF2	chr16:12073030-12073405	GM12878	blood:	n/a	n/a
3	CHD1	chr16:12073069-12073373	GM12878	blood:	n/a	n/a
4	EP300	chr16:12073233-12073433	GM12878	blood:	n/a	chr16:12073393-12073402
5	BCL3	chr16:12073062-12073403	GM12878	blood:	n/a	chr16:12073285-12073294 chr16:12073333-12073342
6	ZNF384	chr16:12072991-12073406	GM12878	blood:	n/a	n/a
7	SPI1	chr16:12073148-12073373	GM12878	blood:	n/a	chr16:12073283-12073292 chr16:12073281-12073294
8	PAX5	chr16:12073234-12073811	GM12878	blood:	n/a	n/a
9	FOXM1	chr16:12073037-12073571	GM12878	blood:	n/a	n/a
10	NFIC	chr16:12073008-12073544	GM12878	blood:	n/a	n/a
11	EBF1	chr16:12073164-12073459	GM12878	blood:	n/a	n/a
12	RELA	chr16:12073040-12073485	GM19099	blood:	n/a	n/a
13	RELA	chr16:12073147-12073586	GM12891	blood:	n/a	n/a
14	RELA	chr16:12073114-12073501	GM12878	blood:	n/a	n/a
15	ATF2	chr16:12073059-12073557	GM12878	blood:	n/a	n/a
16	CUX1	chr16:12073154-12073465	GM12878	blood:	n/a	n/a
17	RUNX3	chr16:12073036-12073538	GM12878	blood:	n/a	n/a
18	MAZ	chr16:12073294-12073364	GM12878	blood:	n/a	n/a
19	EP300	chr16:12073261-12073359	GM12878	blood:	n/a	n/a
20	RUNX3	chr16:12073141-12073432	GM12878	blood:	n/a	n/a
21	SMC3	chr16:12073254-12073411	GM12878	blood:	n/a	n/a
22	SPI1	chr16:12073155-12073464	GM12891	blood:	n/a	chr16:12073283-12073292 chr16:12073281-12073294 chr16:12073392-12073405
23	PAX5	chr16:12073344-12073724	GM12878	blood:	n/a	n/a
24	BHLHE40	chr16:12073156-12073367	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12071974..12074044-chr16:12076209..12078195,2	K562	blood:
2	chr16:12006532..12011371-chr16:12068460..12073371,6	K562	blood:

Variant related genes	Relation type
ENSG00000260488	TF binding region
ENSG00000234719	TF binding region
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11639821	0.82[MEX][hapmap]
rs378372	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs393276	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs417938	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs426424	1.00[CHB][hapmap]
rs442234	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs446289	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7197059	0.86[MEX][hapmap]
rs8051298	0.85[MEX][hapmap]
rs86428	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv527197	chr16:12071341-12073800	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs436838	RP11-166B2.1	cis	Whole Blood	GTEx
rs436838	RP11-166B2.1	cis	Esophagus Muscularis	GTEx
rs436838	TNFRSF17	cis	parietal	SCAN
rs436838	GSPT1	cis	parietal	SCAN
rs436838	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs436838	RP11-166B2.1	cis	Artery Tibial	GTEx
rs436838	TNFRSF17	cis	cerebellum	SCAN
rs436838	RP11-166B2.1	cis	Nerve Tibial	GTEx
rs436838	RP11-166B2.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071600-12083200	Weak transcription	Left Ventricle	heart
3	chr16:12071800-12078000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:12071800-12079400	Weak transcription	Lung	lung
5	chr16:12071800-12079800	Weak transcription	Aorta	Aorta
6	chr16:12071800-12083200	Weak transcription	Spleen	Spleen
7	chr16:12071800-12088200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
9	chr16:12072000-12086200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr16:12072000-12087200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr16:12072000-12088200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr16:12072000-12093600	Weak transcription	Fetal Stomach	stomach
13	chr16:12072200-12073800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr16:12072200-12073800	Weak transcription	Brain Germinal Matrix	brain
15	chr16:12072200-12075200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:12072200-12077200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr16:12072200-12084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr16:12072200-12087400	Weak transcription	Fetal Thymus	thymus
19	chr16:12072200-12088200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr16:12072200-12088200	Weak transcription	Right Ventricle	heart
21	chr16:12072200-12093800	Weak transcription	Thymus	Thymus
22	chr16:12072200-12096600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr16:12072400-12073600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:12072400-12077200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr16:12072400-12077200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr16:12072400-12080400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:12072400-12082400	Weak transcription	Placenta	Placenta
29	chr16:12072400-12083200	Weak transcription	Adipose Nuclei	Adipose
30	chr16:12072400-12086200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:12072400-12086200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr16:12072400-12087200	Weak transcription	Primary T cells from cord blood	blood
33	chr16:12072400-12096400	Weak transcription	Ovary	ovary
34	chr16:12072400-12104400	Weak transcription	NHLF	lung
35	chr16:12072600-12073400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr16:12072600-12074000	Weak transcription	HepG2	liver
37	chr16:12072600-12075600	Weak transcription	Fetal Kidney	kidney
38	chr16:12072600-12076200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:12072600-12076800	Enhancers	Primary B cells from cord blood	blood
40	chr16:12072600-12077600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:12072600-12082000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr16:12072600-12082400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:12072600-12086200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr16:12072600-12094000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr16:12072600-12094000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr16:12073200-12073400	Enhancers	Primary B cells from peripheral blood	blood
49	chr16:12073200-12074400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr16:12073200-12074800	Flanking Active TSS	GM12878-XiMat	blood

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