Variant report

Variant	rs7219324
Chromosome Location	chr17:17909775-17909776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr17:17909729-17909865	K562	blood:	n/a	n/a
2	CTCF	chr17:17909762-17909864	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr17:17909717-17909861	K562	blood:	n/a	n/a
4	CTCF	chr17:17909700-17909850	K562	blood:	n/a	n/a
5	CTCF	chr17:17909700-17909850	HBMEC	blood vessel:	n/a	n/a
6	CTCFL	chr17:17909725-17909853	K562	blood:	n/a	n/a
7	MAX	chr17:17909703-17909969	K562	blood:	n/a	n/a
8	CTCF	chr17:17909680-17909830	HRE	kidney:	n/a	n/a
9	CTCF	chr17:17909700-17909850	MCF-7	breast:	n/a	n/a
10	CTCF	chr17:17909700-17909850	NB4	blood:	n/a	n/a
11	CTCFL	chr17:17909730-17909852	K562	blood:	n/a	n/a
12	CTCF	chr17:17909744-17909844	NHEK	skin:	n/a	n/a
13	CTCF	chr17:17909680-17909907	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17903006..17906615-chr17:17908063..17910293,3	K562	blood:
2	chr17:17904155..17906615-chr17:17908063..17910293,2	K562	blood:
3	chr17:17904327..17906012-chr17:17908673..17910250,2	MCF-7	breast:
4	chr17:17901247..17903124-chr17:17907149..17909889,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232344	TF binding region
LRRC48	TF binding region
ENSG00000201378	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11078408	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs11650021	0.86[EUR][1000 genomes]
rs11869491	0.96[EUR][1000 genomes]
rs11870660	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs11871231	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12150369	0.94[EUR][1000 genomes]
rs12939020	0.85[EUR][1000 genomes]
rs12940282	0.81[EUR][1000 genomes]
rs28537385	0.93[EUR][1000 genomes]
rs28555361	0.81[EUR][1000 genomes]
rs2955350	0.88[EUR][1000 genomes]
rs2955353	0.88[EUR][1000 genomes]
rs2955354	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2955355	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955356	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955357	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2955358	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955359	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2955368	0.87[EUR][1000 genomes]
rs2955370	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2955372	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs2955377	0.90[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2955378	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2955380	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2955381	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2955383	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs2955384	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs2955385	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs2974999	0.89[CEU][hapmap]
rs4072738	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072739	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4299203	0.85[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs4365348	0.94[EUR][1000 genomes]
rs4368210	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs4426402	0.89[CEU][hapmap]
rs4459604	0.95[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4506969	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs4584886	0.95[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs4643387	0.85[EUR][1000 genomes]
rs4924832	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs4925133	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4925135	0.88[EUR][1000 genomes]
rs4925136	0.87[EUR][1000 genomes]
rs4925137	0.86[JPT][hapmap]
rs62072048	0.85[EUR][1000 genomes]
rs62072050	0.93[EUR][1000 genomes]
rs6502631	0.92[EUR][1000 genomes]
rs6502632	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs6502633	0.90[EUR][1000 genomes]
rs6502634	0.84[EUR][1000 genomes]
rs6502636	0.94[CEU][hapmap]
rs7207461	0.88[EUR][1000 genomes]
rs7207821	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7209003	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7210400	0.88[EUR][1000 genomes]
rs7211714	0.89[CEU][hapmap]
rs7212167	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs7212447	0.89[CEU][hapmap]
rs7215524	0.93[EUR][1000 genomes]
rs721669	0.89[CEU][hapmap];0.83[YRI][hapmap]
rs7219320	0.80[MEX][hapmap];0.93[TSI][hapmap]
rs7223696	0.93[EUR][1000 genomes]
rs7224047	0.92[EUR][1000 genomes]
rs7406982	0.95[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs7503738	0.89[EUR][1000 genomes]
rs8068175	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs8069811	0.93[EUR][1000 genomes]
rs8070731	0.81[EUR][1000 genomes]
rs8071238	0.85[EUR][1000 genomes]
rs8075189	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs8080602	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs8082590	0.81[EUR][1000 genomes]
rs854763	0.89[CEU][hapmap]
rs854767	0.89[CEU][hapmap]
rs854769	0.89[CEU][hapmap]
rs854790	0.89[CEU][hapmap]
rs854791	0.89[CEU][hapmap]
rs854809	0.89[CEU][hapmap]
rs854814	0.89[CEU][hapmap]
rs854817	0.89[CEU][hapmap]
rs9303144	0.89[CEU][hapmap]
rs9894138	0.88[EUR][1000 genomes]
rs9896837	0.95[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs9897761	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs9899355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911850	0.92[EUR][1000 genomes]
rs9912096	0.93[EUR][1000 genomes]
rs9913277	0.95[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS 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 miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7219324	TOM1L2	cis	cerebellum	SCAN
rs7219324	C17orf39	cis	cerebellum	SCAN
rs7219324	TOM1L2	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17876600-17914600	Weak transcription	Aorta	Aorta
2	chr17:17876800-17912000	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:17886800-17913000	Weak transcription	Fetal Lung	lung
4	chr17:17892400-17910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:17892600-17909800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:17894000-17920600	Weak transcription	Stomach Mucosa	stomach
7	chr17:17894600-17911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:17898000-17910800	Weak transcription	Brain Hippocampus Middle	brain
9	chr17:17898200-17918000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr17:17898200-17918000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:17898400-17910000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:17898400-17911400	Weak transcription	HSMM	muscle
13	chr17:17898600-17909800	Weak transcription	Adipose Nuclei	Adipose
14	chr17:17898600-17909800	Weak transcription	Ovary	ovary
15	chr17:17898600-17910600	Weak transcription	Placenta	Placenta
16	chr17:17898600-17910800	Weak transcription	Esophagus	oesophagus
17	chr17:17898600-17917600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:17903000-17911400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:17903200-17909800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:17903400-17909800	Weak transcription	Liver	Liver
21	chr17:17903600-17913200	Weak transcription	Gastric	stomach
22	chr17:17903600-17913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:17903800-17909800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr17:17904000-17910000	Weak transcription	Fetal Intestine Large	intestine
25	chr17:17904000-17911800	Weak transcription	HepG2	liver
26	chr17:17905000-17910800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:17905000-17912000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:17905800-17909800	Weak transcription	Thymus	Thymus
29	chr17:17905800-17911400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:17906000-17911800	Weak transcription	NHDF-Ad	bronchial
31	chr17:17906000-17912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:17906000-17914800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr17:17906200-17941400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr17:17906400-17910000	Weak transcription	Fetal Thymus	thymus
35	chr17:17906600-17929000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr17:17907400-17913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:17907400-17915800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr17:17907800-17910000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:17907800-17911400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr17:17907800-17915200	Strong transcription	Primary B cells from cord blood	blood
41	chr17:17908000-17913000	Weak transcription	A549	lung
42	chr17:17908000-17915400	Strong transcription	Spleen	Spleen
43	chr17:17908000-17918000	Weak transcription	Brain Germinal Matrix	brain
44	chr17:17908200-17909800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:17908200-17909800	Weak transcription	Dnd41	blood
46	chr17:17908200-17911400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr17:17908200-17912000	Strong transcription	Pancreas	Pancrea
48	chr17:17908200-17912200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr17:17908200-17913800	Strong transcription	Fetal Stomach	stomach
50	chr17:17908200-17914200	Strong transcription	Primary T cells from cord blood	blood

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