Variant report

Variant	rs12760457
Chromosome Location	chr1:114389748-114389749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:107891473..107893309-chr1:114388467..114390772,2	MCF-7	breast:
2	chr1:114388839..114391428-chr1:114410899..114412485,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10127930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10489936	0.87[EUR][1000 genomes]
rs1080307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1217384	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217394	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs12723023	0.82[EUR][1000 genomes]
rs12729708	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12730735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731010	0.85[EUR][1000 genomes]
rs12734625	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12735104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12739970	0.82[EUR][1000 genomes]
rs12746609	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12748727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752932	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12753075	0.84[EUR][1000 genomes]
rs12753351	0.87[EUR][1000 genomes]
rs12758546	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13374352	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1539438	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs17274550	0.88[EUR][1000 genomes]
rs17274620	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17274634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs17359302	0.88[EUR][1000 genomes]
rs17462614	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17509390	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1885454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2040040	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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2359173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2359174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2476601	1.00[LWK][hapmap]
rs34042871	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34341173	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34649199	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34698891	0.87[EUR][1000 genomes]
rs34857922	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34877889	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35320278	0.88[EUR][1000 genomes]
rs35383900	0.87[EUR][1000 genomes]
rs35836713	0.88[EUR][1000 genomes]
rs36115604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747998	0.88[EUR][1000 genomes]
rs3748003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3752953	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs3761931	0.87[EUR][1000 genomes]
rs3789595	0.88[EUR][1000 genomes]
rs3789599	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs3789607	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[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61817579	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817586	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817617	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61819423	0.84[EUR][1000 genomes]
rs61819424	0.81[EUR][1000 genomes]
rs61820162	0.87[EUR][1000 genomes]
rs6668829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674848	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];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6703387	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[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71662845	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7533391	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549685	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7555354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9803891	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12760457	CD58	cis	cerebellum	SCAN

Chromatin state (count:34 , 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	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:114361800-114390400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:114377600-114392800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:114377600-114392800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:114378000-114402600	Weak transcription	Colonic Mucosa	Colon
10	chr1:114379000-114393000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:114379200-114390400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr1:114379200-114391600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:114379800-114391400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:114381000-114390000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:114382200-114390200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:114382600-114392000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:114384800-114390200	Weak transcription	Thymus	Thymus
18	chr1:114385800-114391800	Strong transcription	Primary B cells from cord blood	blood
19	chr1:114387600-114391600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:114387800-114390800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:114388000-114393200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:114388200-114390200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:114388400-114391400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:114388800-114389800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:114388800-114390200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:114389000-114391800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:114389200-114389800	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr1:114389200-114390000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:114389200-114390800	ZNF genes & repeats	GM12878-XiMat	blood
30	chr1:114389200-114391200	Strong transcription	Fetal Thymus	thymus
31	chr1:114389200-114391400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:114389200-114391600	Strong transcription	Dnd41	blood
33	chr1:114389400-114389800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
34	chr1:114389600-114391400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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