Variant report

Variant	rs4646340
Chromosome Location	chr17:17494015-17494016
allele	A/G
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	TCF12	chr17:17493783-17496081	A549	lung:	n/a	n/a
2	MAX	chr17:17493731-17494072	K562	blood:	n/a	n/a
3	MXI1	chr17:17493375-17496079	IMR90	lung:	n/a	n/a
4	MAX	chr17:17493765-17496079	A549	lung:	n/a	chr17:17495318-17495328 chr17:17494690-17494699
5	ARID3A	chr17:17493850-17494070	HepG2	liver:	n/a	n/a
6	WRNIP1	chr17:17493984-17494155	GM12878	blood:	n/a	n/a
7	SREBP1	chr17:17493979-17495978	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:17493477-17494039	HepG2	liver:	n/a	n/a
9	MAX	chr17:17493723-17495882	HepG2	liver:	n/a	chr17:17495318-17495328 chr17:17494690-17494699
10	JUN	chr17:17493855-17496121	K562	blood:	n/a	chr17:17494748-17494757

No.	Distal block	Cell Line	Cell type
1	chr17:17485277..17487329-chr17:17493832..17495803,2	MCF-7	breast:
2	chr17:17485257..17488708-chr17:17493396..17495920,3	K562	blood:
3	chr17:17481596..17485305-chr17:17490709..17495159,5	MCF-7	breast:
4	chr17:17417278..17420062-chr17:17491860..17494692,3	MCF-7	breast:
5	chr17:17480072..17482528-chr17:17493213..17495620,3	MCF-7	breast:
6	chr17:17398240..17400896-chr17:17493826..17497836,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264666	TF binding region
ENSG00000133027	Chromatin interaction
ENSG00000206730	Chromatin interaction
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11078389	0.88[CEU][hapmap]
rs11078390	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11654842	0.86[CEU][hapmap]
rs11867208	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11869492	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12453139	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12936201	0.94[ASN][1000 genomes]
rs12948060	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs1809206	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124344	0.81[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2350631	0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4244596	0.88[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs4244598	0.88[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs4646341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646347	0.81[AMR][1000 genomes]
rs4646350	0.88[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs4646351	0.81[AMR][1000 genomes]
rs4646356	0.85[CEU][hapmap]
rs4646357	0.80[AMR][1000 genomes]
rs4646359	0.85[CEU][hapmap]
rs4646365	0.82[CEU][hapmap]
rs4646370	0.81[AMR][1000 genomes]
rs4646372	0.81[AMR][1000 genomes]
rs4925027	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs62066209	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6502609	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7209113	0.81[AMR][1000 genomes]
rs7215833	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729974	0.81[AMR][1000 genomes]
rs729975	0.88[CEU][hapmap]
rs8082417	0.88[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs897451	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs9890064	0.90[JPT][hapmap]
rs9895955	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv1062052	chr17:17461050-17507199	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv543237	chr17:17461050-17507199	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv833383	chr17:17464635-17509138	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4646340	RAI1	cis	parietal	SCAN
rs4646340	SNORD49B	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17483600-17494200	Weak transcription	Gastric	stomach
2	chr17:17493000-17494400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:17493000-17494400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:17493200-17494200	Enhancers	Lung	lung
5	chr17:17493200-17494400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:17493400-17494200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr17:17493400-17494200	Enhancers	Right Atrium	heart
8	chr17:17493400-17494400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr17:17493400-17494400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:17493400-17494400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:17493400-17494400	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr17:17493400-17494400	Flanking Active TSS	Dnd41	blood
13	chr17:17493400-17494600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr17:17493400-17494600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:17493400-17494600	Flanking Active TSS	K562	blood
16	chr17:17493600-17494200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:17493600-17494200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:17493600-17494200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:17493600-17494200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr17:17493600-17494200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr17:17493600-17494200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr17:17493600-17494200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:17493600-17494200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr17:17493600-17494200	Enhancers	Esophagus	oesophagus
25	chr17:17493600-17494200	Flanking Active TSS	Fetal Heart	heart
26	chr17:17493600-17494200	Enhancers	Stomach Mucosa	stomach
27	chr17:17493600-17494200	Flanking Active TSS	A549	lung
28	chr17:17493600-17494200	Flanking Active TSS	Hela-S3	cervix
29	chr17:17493600-17494400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:17493600-17494400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:17493600-17494400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr17:17493600-17494400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr17:17493600-17494400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:17493600-17494400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr17:17493600-17494400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr17:17493600-17494400	Enhancers	Spleen	Spleen
37	chr17:17493600-17494400	Flanking Active TSS	NHDF-Ad	bronchial
38	chr17:17493600-17494400	Flanking Active TSS	NHLF	lung
39	chr17:17493600-17494600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:17493600-17494600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:17493600-17494600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:17493600-17494600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:17493600-17494600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr17:17493600-17494600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr17:17493600-17494600	Flanking Active TSS	Fetal Stomach	stomach
46	chr17:17493600-17494600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr17:17493600-17494600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr17:17493600-17494600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr17:17493600-17494600	Flanking Active TSS	HMEC	breast
50	chr17:17493600-17494600	Flanking Active TSS	HSMM	muscle

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