Variant report

Variant	rs7223246
Chromosome Location	chr17:45759767-45759768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45749677..45752105-chr17:45758082..45761229,3	MCF-7	breast:
2	chr17:45758194..45759902-chr17:45762797..45765497,2	K562	blood:
3	chr17:45759177..45766275-chr17:45767435..45773662,12	K562	blood:
4	chr17:45752623..45755412-chr17:45757645..45762048,4	K562	blood:
5	chr17:45759280..45761453-chr17:45769227..45771829,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198933	Chromatin interaction
ENSG00000108424	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2317826	0.84[ASW][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4580230	0.83[AFR][1000 genomes]
rs4794047	0.91[LWK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7210738	0.80[LWK][hapmap]
rs9905583	0.82[AFR][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	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
2	esv1811231	chr17:45520374-45764956	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1813964	chr17:45520374-45764956	Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv2758458	chr17:45520374-45764956	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv2758693	chr17:45520374-45764956	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv428344	chr17:45520374-45764956	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv978435	chr17:45758314-45761310	Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7223246	C17orf57	cis	cerebellum	SCAN
rs7223246	VPS25	cis	cerebellum	SCAN
rs7223246	RAB5C	cis	parietal	SCAN
rs7223246	C17orf57	cis	parietal	SCAN
rs7223246	MPP3	cis	cerebellum	SCAN
rs7223246	WNT3	cis	parietal	SCAN
rs7223246	MGMT	trans	lymphoblastoid	seeQTL
rs7223246	C17orf65	cis	cerebellum	SCAN
rs7223246	CDK5RAP3	cis	cerebellum	SCAN
rs7223246	DBF4B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45728800-45762800	Strong transcription	Fetal Stomach	stomach
2	chr17:45728800-45765600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr17:45729200-45760400	Strong transcription	Fetal Muscle Leg	muscle
4	chr17:45729200-45760600	Strong transcription	Fetal Brain Female	brain
5	chr17:45729200-45763800	Strong transcription	Placenta	Placenta
6	chr17:45729600-45762600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:45729800-45761600	Strong transcription	HSMM	muscle
8	chr17:45730400-45764800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:45730400-45765000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:45730800-45760600	Strong transcription	Lung	lung
11	chr17:45731200-45762200	Strong transcription	Fetal Lung	lung
12	chr17:45731200-45763800	Strong transcription	K562	blood
13	chr17:45731400-45762000	Strong transcription	NH-A	brain
14	chr17:45732400-45762600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr17:45732600-45760200	Strong transcription	Brain Germinal Matrix	brain
16	chr17:45732600-45760400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:45732600-45762000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:45732600-45762200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:45732800-45760200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:45732800-45760600	Strong transcription	Fetal Intestine Large	intestine
21	chr17:45732800-45762200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:45732800-45762200	Strong transcription	Adipose Nuclei	Adipose
23	chr17:45732800-45762600	Strong transcription	Brain Anterior Caudate	brain
24	chr17:45733000-45761600	Strong transcription	HepG2	liver
25	chr17:45733000-45763600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:45733200-45760200	Strong transcription	Brain Cingulate Gyrus	brain
27	chr17:45733200-45760400	Strong transcription	Hela-S3	cervix
28	chr17:45733200-45762400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr17:45733200-45763400	Strong transcription	NHEK	skin
30	chr17:45733200-45765000	Strong transcription	HMEC	breast
31	chr17:45736200-45763600	Strong transcription	Dnd41	blood
32	chr17:45737000-45762400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:45737800-45762600	Strong transcription	Thymus	Thymus
34	chr17:45737800-45764200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr17:45738000-45760200	Strong transcription	Rectal Smooth Muscle	rectum
36	chr17:45738000-45762600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:45738000-45763800	Strong transcription	Liver	Liver
38	chr17:45738400-45762800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr17:45738400-45763600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr17:45738400-45765600	Strong transcription	Primary T cells from cord blood	blood
41	chr17:45738600-45762600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr17:45738800-45762600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:45739000-45760400	Strong transcription	Ovary	ovary
44	chr17:45739000-45760400	Strong transcription	Spleen	Spleen
45	chr17:45740000-45763400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:45741600-45762200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr17:45741600-45763600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr17:45741800-45760200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr17:45741800-45763400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:45742000-45764800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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