Variant report

Variant	rs9662664
Chromosome Location	chr1:153656352-153656353
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153651109..153660855-chr1:153698392..153702896,14	MCF-7	breast:
2	chr1:153649941..153652996-chr1:153654947..153657663,3	K562	blood:
3	chr1:153653996..153656594-chr1:153656905..153658985,2	MCF-7	breast:
4	chr1:153654218..153657204-chr1:153660557..153664055,3	MCF-7	breast:
5	chr1:153650729..153654060-chr1:153654100..153656603,4	MCF-7	breast:
6	chr1:153648584..153651991-chr1:153654471..153657777,3	MCF-7	breast:
7	chr1:153640859..153647825-chr1:153650423..153657512,10	K562	blood:
8	chr1:153640044..153642973-chr1:153654188..153656632,2	K562	blood:
9	chr1:153652339..153654108-chr1:153654445..153656447,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143621	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000169418	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10797056	0.88[JPT][hapmap]
rs10797096	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908848	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265625	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265633	0.90[ASN][1000 genomes]
rs11588347	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12139953	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12564925	0.88[JPT][hapmap]
rs12730186	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12755890	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1888115	0.88[JPT][hapmap]
rs2274739	0.88[JPT][hapmap]
rs2274740	0.88[JPT][hapmap]
rs28380060	0.88[JPT][hapmap]
rs28518786	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28580554	0.88[JPT][hapmap]
rs28754733	0.85[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs3790411	0.82[JPT][hapmap]
rs3790412	0.88[JPT][hapmap]
rs3795396	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs3806233	0.85[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3806234	0.90[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs3818632	0.88[JPT][hapmap]
rs3828031	0.88[JPT][hapmap]
rs3862047	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4072425	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs4310476	0.85[AMR][1000 genomes]
rs4351684	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs4515830	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs4845563	0.83[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845564	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55772653	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427640	0.82[ASN][1000 genomes]
rs66721814	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6674929	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7345	0.90[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7934	0.88[JPT][hapmap]
rs913861	0.88[JPT][hapmap]
rs9330298	0.81[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9661993	0.95[ASN][1000 genomes]
rs9700179	0.82[TSI][hapmap]
rs9700928	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs9726753	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription 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	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh 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	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9662664	SNAPIN	cis	lymphoblastoid	seeQTL
rs9662664	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs9662664	DCST2	cis	parietal	SCAN
rs9662664	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs9662664	CTSS	cis	parietal	SCAN
rs9662664	S100A2	cis	cerebellum	SCAN
rs9662664	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs9662664	S100A9	cis	parietal	SCAN
rs9662664	S100A16	cis	parietal	SCAN
rs9662664	S100A13	cis	lymphoblastoid	seeQTL
rs9662664	S100A16	cis	cerebellum	SCAN
rs9662664	S100A13	cis	parietal	SCAN
rs9662664	SLC27A3	cis	cerebellum	SCAN
rs9662664	S100A10	cis	cerebellum	SCAN
rs9662664	FLG	cis	cerebellum	SCAN
rs9662664	SCNM1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153652400-153664600	Weak transcription	Gastric	stomach
2	chr1:153652400-153669800	Weak transcription	Pancreas	Pancrea
3	chr1:153653000-153669800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:153653200-153664000	Weak transcription	Left Ventricle	heart
5	chr1:153653200-153669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:153653400-153663200	Strong transcription	Ovary	ovary
7	chr1:153653600-153656800	Genic enhancers	Adipose Nuclei	Adipose
8	chr1:153653600-153659600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:153653800-153666400	Strong transcription	Lung	lung
10	chr1:153653800-153669400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:153654000-153656400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:153654400-153657400	Weak transcription	Right Atrium	heart
13	chr1:153654400-153669200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:153654400-153669400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:153654800-153659400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:153655000-153656400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:153655400-153656600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:153655400-153658000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:153655400-153660800	Weak transcription	Spleen	Spleen
20	chr1:153655400-153669800	Weak transcription	Esophagus	oesophagus
21	chr1:153655800-153657800	Strong transcription	Right Ventricle	heart
22	chr1:153656000-153656600	Genic enhancers	Fetal Kidney	kidney
23	chr1:153656000-153656800	Genic enhancers	Aorta	Aorta
24	chr1:153656000-153657400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:153656000-153657400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:153656200-153656400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:153656200-153656400	Genic enhancers	Hela-S3	cervix
28	chr1:153656200-153656800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:153656200-153659400	Weak transcription	H1 Cell Line	embryonic stem cell

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