Variant report

Variant	rs7216411
Chromosome Location	chr17:46088944-46088945
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46026531..46027246-chr17:46088402..46089166,2	MCF-7	breast:
2	chr17:46082138..46085866-chr17:46087014..46089274,3	K562	blood:
3	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
4	chr17:45973275..45976103-chr17:46088600..46091071,2	K562	blood:
5	chr17:46065449..46067684-chr17:46085725..46089051,3	K562	blood:
6	chr17:46055207..46056272-chr17:46088652..46089300,3	MCF-7	breast:
7	chr17:46088611..46089553-chr17:46102607..46103180,2	MCF-7	breast:
8	chr17:45946630..45948795-chr17:46087511..46090189,2	K562	blood:
9	chr17:46083495..46085251-chr17:46088576..46090117,2	MCF-7	breast:
10	chr17:45973448..45975240-chr17:46087666..46090341,2	MCF-7	breast:
11	chr17:46046725..46049837-chr17:46087369..46090081,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1317850	0.84[ASW][hapmap];0.91[CEU][hapmap];0.89[TSI][hapmap]
rs2256020	0.84[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[MEX][hapmap]
rs2525083	0.83[CHB][hapmap]
rs2525097	0.91[CHB][hapmap]
rs2525104	0.93[ASN][1000 genomes]
rs2597178	0.87[CHB][hapmap]
rs2737	0.87[CHB][hapmap]
rs2905855	0.84[CHD][hapmap]
rs736387	0.84[ASW][hapmap];0.87[CHB][hapmap]
rs757352	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8076163	0.91[CEU][hapmap];0.89[TSI][hapmap]

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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7216411	DNAJC7	cis	cerebellum	SCAN
rs7216411	DUSP3	cis	parietal	SCAN
rs7216411	VAT1	cis	cerebellum	SCAN
rs7216411	CDK5RAP3	cis	Whole Blood	GTEx
rs7216411	NFE2L1	cis	cerebellum	SCAN
rs7216411	ATP6V0A1	cis	parietal	SCAN
rs7216411	SNX11	cis	brain	BrainEAC

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46081000-46089000	Weak transcription	Brain Angular Gyrus	brain
2	chr17:46082600-46090000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:46083000-46089000	Weak transcription	HMEC	breast
4	chr17:46083000-46089200	Weak transcription	HSMMtube	muscle
5	chr17:46083800-46089200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:46084800-46089000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:46087200-46089200	Enhancers	Fetal Brain Male	brain
8	chr17:46087400-46089000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:46088600-46089000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr17:46088600-46089000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr17:46088600-46089000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr17:46088600-46089400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:46088600-46089400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:46088600-46089400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:46088600-46089400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:46088800-46089000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46088800-46089000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:46088800-46089000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr17:46088800-46089000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr17:46088800-46089000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46088800-46089000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:46088800-46089000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:46088800-46089000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:46088800-46089000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr17:46088800-46089000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr17:46088800-46089000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr17:46088800-46089000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:46088800-46089000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
29	chr17:46088800-46089000	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
30	chr17:46088800-46089000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr17:46088800-46089000	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
32	chr17:46088800-46089000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:46088800-46089000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:46088800-46089000	Active TSS	Brain Anterior Caudate	brain
35	chr17:46088800-46089000	Active TSS	Brain Cingulate Gyrus	brain
36	chr17:46088800-46089000	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr17:46088800-46089000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:46088800-46089000	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
39	chr17:46088800-46089000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
40	chr17:46088800-46089000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr17:46088800-46089000	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr17:46088800-46089000	Bivalent Enhancer	Fetal Intestine Small	intestine
43	chr17:46088800-46089000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
44	chr17:46088800-46089000	Bivalent Enhancer	Fetal Stomach	stomach
45	chr17:46088800-46089000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
46	chr17:46088800-46089000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr17:46088800-46089000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
48	chr17:46088800-46089000	Enhancers	HSMM	muscle
49	chr17:46088800-46089000	Enhancers	NH-A	brain
50	chr17:46088800-46089000	Flanking Active TSS	NHEK	skin

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