Variant report

Variant	rs7521948
Chromosome Location	chr1:179995975-179995976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179995799..179998188-chr1:180047230..180050117,2	MCF-7	breast:
2	chr1:179994934..179997849-chr1:180033158..180035390,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10798729	0.80[JPT][hapmap]
rs10913916	0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10913917	0.81[JPT][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12075450	0.81[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12091685	0.90[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs12094391	0.86[EUR][1000 genomes]
rs16855164	0.98[ASN][1000 genomes]
rs1981314	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2319676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2319677	0.86[JPT][hapmap]
rs2319773	0.86[ASN][1000 genomes]
rs2477106	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2477107	0.91[ASN][1000 genomes]
rs2477109	0.89[ASN][1000 genomes]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2477113	0.88[ASN][1000 genomes]
rs2477115	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2477117	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2483622	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2501608	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501614	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2501615	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2501618	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501619	0.87[ASN][1000 genomes]
rs2501621	0.93[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2762859	0.81[JPT][hapmap]
rs3123521	0.93[ASN][1000 genomes]
rs3767201	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs3818999	0.81[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.93[JPT][hapmap]
rs4147170	0.86[JPT][hapmap]
rs4256775	0.93[JPT][hapmap]
rs4263962	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4379644	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4622030	0.86[JPT][hapmap]
rs4651055	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4652461	1.00[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652464	0.86[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.81[JPT][hapmap]
rs510209	0.81[JPT][hapmap]
rs551607	0.81[ASW][hapmap]
rs6425602	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425603	0.93[JPT][hapmap]
rs6425606	0.90[ASW][hapmap];0.85[JPT][hapmap]
rs6425607	0.86[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6659911	0.94[ASN][1000 genomes]
rs6660984	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6676989	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6692394	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9286932	0.93[JPT][hapmap]
rs9425849	0.93[JPT][hapmap]
rs9425852	0.95[ASN][1000 genomes]
rs9425853	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.90[ASN][1000 genomes]
rs9425858	0.87[ASN][1000 genomes]
rs9425859	0.80[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7521948	TOR1AIP2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:179971600-179997400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:179973000-180010800	Weak transcription	Psoas Muscle	Psoas
7	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:179979400-179999600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:179979600-180002000	Strong transcription	Fetal Intestine Large	intestine
10	chr1:179979800-179998000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:179979800-179998600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:179979800-179999000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:179979800-179999400	Strong transcription	Fetal Thymus	thymus
14	chr1:179979800-180008400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:179980200-180007800	Strong transcription	Primary B cells from cord blood	blood
16	chr1:179980400-179998200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:179980400-180027400	Strong transcription	Dnd41	blood
18	chr1:179980600-179997400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:179980600-179999000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:179980600-179999200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:179980600-179999800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:179980600-180008000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:179981000-179997000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:179981000-180027200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:179981200-179996400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:179981200-179996800	Strong transcription	Adipose Nuclei	Adipose
28	chr1:179981600-179997400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:179981600-179997600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:179981600-179998000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:179981600-180012000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:179982400-179996400	Strong transcription	Placenta	Placenta
33	chr1:179982400-179998000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:179982400-179999000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:179983000-179996000	Strong transcription	Liver	Liver
36	chr1:179983000-179996400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:179983000-179996600	Strong transcription	Hela-S3	cervix
38	chr1:179983000-179998800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:179983000-179999000	Strong transcription	Primary T cells from cord blood	blood
40	chr1:179983200-179996000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:179983200-179996800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:179983200-179998000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:179985000-179996000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:179985600-180024800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:179986400-179996200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:179987600-179996800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr1:179989000-180000000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:179989000-180008800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:179989200-179999800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood

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