Variant report

Variant	rs13330399
Chromosome Location	chr16:12161649-12161650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:12043208..12044500-chr16:12161423..12162347,8	K562	blood:
2	chr16:12007976..12010590-chr16:12160266..12161829,2	K562	blood:
3	chr16:12008327..12011820-chr16:12160146..12163377,5	MCF-7	breast:
4	chr16:11965136..11965755-chr16:12161438..12161952,2	K562	blood:
5	chr16:12065623..12066578-chr16:12161490..12162277,2	K562	blood:
6	chr16:12008315..12010617-chr16:12160352..12162874,2	MCF-7	breast:
7	chr16:12151950..12154573-chr16:12160547..12163512,2	MCF-7	breast:
8	chr16:12043121..12044152-chr16:12161482..12162455,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11075049	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12708744	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12708745	0.88[AFR][1000 genomes]
rs12708746	0.92[AFR][1000 genomes]
rs13331254	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13338070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869808	0.89[AFR][1000 genomes]
rs34352258	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350211	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851011	0.93[YRI][hapmap]
rs3894905	1.00[CHB][hapmap]
rs7195019	0.93[AFR][1000 genomes]
rs8050180	0.84[CHB][hapmap];0.93[YRI][hapmap]
rs8055516	0.90[AFR][1000 genomes]
rs8062015	0.90[AFR][1000 genomes]
rs9939383	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13330399	TNFRSF17	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr16:12139400-12172600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr16:12144200-12169400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr16:12146000-12183400	Weak transcription	Fetal Intestine Large	intestine
6	chr16:12146200-12163000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:12146600-12162000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:12148000-12183400	Weak transcription	Fetal Lung	lung
9	chr16:12149800-12172600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:12153400-12177200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr16:12153800-12168800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:12155400-12163200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr16:12155400-12172400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr16:12155400-12172600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr16:12155600-12172400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:12155600-12172600	Weak transcription	Fetal Intestine Small	intestine
17	chr16:12155800-12162800	Weak transcription	GM12878-XiMat	blood
18	chr16:12155800-12169200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:12155800-12169800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
21	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
22	chr16:12156600-12162600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr16:12156800-12162800	Weak transcription	Fetal Muscle Leg	muscle
24	chr16:12156800-12173200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:12157000-12161800	Weak transcription	Brain Hippocampus Middle	brain
26	chr16:12157000-12162800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr16:12157000-12163000	Weak transcription	Liver	Liver
28	chr16:12157000-12163200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr16:12157000-12169800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr16:12157000-12175800	Weak transcription	Fetal Kidney	kidney
31	chr16:12157000-12181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr16:12157000-12181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr16:12157200-12162800	Weak transcription	NHEK	skin
34	chr16:12157200-12163000	Weak transcription	Brain Substantia Nigra	brain
35	chr16:12157200-12163000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr16:12157200-12171800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr16:12157200-12172200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:12157200-12172600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:12157200-12172600	Weak transcription	Aorta	Aorta
40	chr16:12157200-12172600	Weak transcription	Brain Angular Gyrus	brain
41	chr16:12157200-12172800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr16:12157200-12172800	Weak transcription	Gastric	stomach
43	chr16:12157200-12173800	Weak transcription	Osteobl	bone
44	chr16:12157200-12183200	Weak transcription	NHLF	lung
45	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:12157600-12162800	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:12157600-12172400	Weak transcription	Esophagus	oesophagus
48	chr16:12157600-12172400	Weak transcription	NHDF-Ad	bronchial
49	chr16:12157800-12162800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr16:12157800-12163000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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