Variant report

Variant	rs2476599
Chromosome Location	chr1:114363459-114363460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114360163..114364211-chr1:114365075..114367436,3	K562	blood:
2	chr1:114363157..114365408-chr1:114367840..114369479,2	K562	blood:
3	chr1:114361850..114364464-chr1:114444259..114447022,2	MCF-7	breast:
4	chr1:114361991..114364301-chr1:114365231..114367809,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000134262	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10858015	0.89[ASN][1000 genomes]
rs11102678	1.00[ASW][hapmap];0.81[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1146183	0.81[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs1146184	0.81[CEU][hapmap]
rs1146185	0.81[ASW][hapmap];0.94[GIH][hapmap]
rs12144309	0.86[GIH][hapmap]
rs1217375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1217378	0.84[AFR][1000 genomes]
rs1217379	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs1217382	0.90[JPT][hapmap]
rs1217393	0.91[JPT][hapmap]
rs1217397	0.90[JPT][hapmap]
rs1217401	0.90[JPT][hapmap]
rs1217403	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1217405	0.89[AFR][1000 genomes]
rs1217406	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1217408	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1217411	0.82[AFR][1000 genomes]
rs1217414	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1217417	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1217418	0.81[ASW][hapmap];0.97[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs1217419	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1217420	0.82[AFR][1000 genomes]
rs1217423	0.82[JPT][hapmap]
rs1230673	0.87[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs1230681	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1230684	1.00[ASN][1000 genomes]
rs1310182	0.91[AFR][1000 genomes]
rs13524	0.93[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs1624335	0.94[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs1743594	0.94[ASW][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap]
rs1746857	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1746860	0.90[JPT][hapmap]
rs1935836	0.81[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1970559	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2040041	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2185827	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2476600	0.93[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs2476602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2476604	0.93[AFR][1000 genomes]
rs2636000	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636003	0.87[ASW][hapmap];0.81[CEU][hapmap];0.94[GIH][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs2797416	0.93[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs3789597	0.86[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs3789598	0.91[YRI][hapmap]
rs3789600	0.87[ASW][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4991898	0.87[AFR][1000 genomes]
rs6537798	0.87[ASW][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs7555634	0.93[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs971173	0.90[JPT][hapmap]

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

No data

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	chr1:114355800-114364200	Weak transcription	Primary T cells from cord blood	blood
4	chr1:114355800-114364400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:114355800-114376600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:114355800-114376800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:114356000-114364000	Weak transcription	Thymus	Thymus
10	chr1:114356000-114370200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:114356000-114370600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:114356000-114376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:114356000-114377400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:114356200-114365000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:114356200-114365000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:114356200-114370200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:114356400-114364400	Weak transcription	Dnd41	blood
18	chr1:114357000-114392200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:114357200-114377600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:114357200-114377800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:114358000-114369200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:114358400-114377600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:114358600-114377600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:114359200-114368000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:114359400-114364200	Weak transcription	GM12878-XiMat	blood
26	chr1:114361200-114366800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:114361600-114365000	Weak transcription	Fetal Thymus	thymus
28	chr1:114361600-114365800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:114361800-114365400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:114361800-114390400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:114362200-114367400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:114362600-114369200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:114363200-114366600	Strong transcription	Primary B cells from cord blood	blood
34	chr1:114363400-114370200	Weak transcription	K562	blood

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