Variant report

Variant	rs7555634
Chromosome Location	chr1:114367116-114367117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114366498..114370144-chr1:114371156..114374268,3	MCF-7	breast:
2	chr1:114366150..114373270-chr1:114373613..114381825,12	MCF-7	breast:
3	chr1:114360163..114364211-chr1:114365075..114367436,3	K562	blood:
4	chr1:114353911..114356847-chr1:114364689..114367754,3	K562	blood:
5	chr1:114367040..114367747-chr1:114505777..114506431,2	MCF-7	breast:
6	chr1:114352743..114357488-chr1:114365626..114369516,6	MCF-7	breast:
7	chr1:114361991..114364301-chr1:114365231..114367809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163349	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134242	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10858016	0.87[ASN][1000 genomes]
rs11102678	0.85[LWK][hapmap]
rs1111695	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs1217375	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs1217378	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217385	0.82[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217404	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217405	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217406	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217408	0.83[YRI][hapmap]
rs1217409	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217411	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217418	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217419	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217420	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230673	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs1230682	0.97[ASN][1000 genomes]
rs1230686	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1235005	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1310182	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13524	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs1539437	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1624335	0.81[ASW][hapmap]
rs1743594	0.81[ASW][hapmap]
rs1970559	0.93[LWK][hapmap]
rs2040041	0.86[LWK][hapmap]
rs2185971	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2273758	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2476599	0.93[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs2476600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476602	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs2476604	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2488458	0.86[ASW][hapmap]
rs2636003	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs2797409	0.85[ASW][hapmap];0.81[LWK][hapmap]
rs2797414	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs2797416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789598	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789600	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4991898	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537798	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665194	0.82[CEU][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672018	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7556622	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS 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	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers 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 target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7555634	MAGI3	cis	cerebellum	SCAN
rs7555634	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
3	chr1:114355800-114376600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:114355800-114376800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:114356000-114370200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:114356000-114370600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:114356000-114376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:114356000-114377400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:114356200-114370200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:114357200-114377600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:114357200-114377800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:114358000-114369200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:114358400-114377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:114358600-114377600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:114359200-114368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:114361800-114390400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:114362200-114367400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:114362600-114369200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:114363400-114370200	Weak transcription	K562	blood
23	chr1:114365000-114368200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:114365200-114368200	Weak transcription	Lung	lung
25	chr1:114365200-114376400	Weak transcription	Dnd41	blood
26	chr1:114365400-114377600	Strong transcription	GM12878-XiMat	blood
27	chr1:114366200-114368000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:114366200-114368000	Weak transcription	Thymus	Thymus
29	chr1:114366400-114368200	Weak transcription	Fetal Thymus	thymus
30	chr1:114366400-114376800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:114366600-114368000	Weak transcription	Primary B cells from cord blood	blood
32	chr1:114366600-114368800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:114366600-114376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:114366800-114367600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:114366800-114379600	Weak transcription	Primary T cells from cord blood	blood

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