Variant report

Variant	rs879963
Chromosome Location	chr1:190141891-190141892
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	chr1:190124803..190126326-chr1:190141675..190144317,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10047048	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10218638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10494632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800937	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10920611	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10920654	0.86[MEX][hapmap]
rs10920655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10920677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10920680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10920692	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.81[YRI][hapmap]
rs12057206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059561	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12072689	0.81[ASN][1000 genomes]
rs12072690	0.81[ASN][1000 genomes]
rs12073139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12073296	0.81[ASN][1000 genomes]
rs12076854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12090879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093349	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12095582	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406050	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12407537	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1333319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374608	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1342909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1539473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540513	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap]
rs1557188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1592245	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16832159	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16832195	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16832220	0.81[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[YRI][hapmap]
rs1831784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1832963	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970123	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065557	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104927	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293451	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2418886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2419063	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.81[MEX][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs35941447	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762299	0.90[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap]
rs3849278	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap]
rs4373764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4399162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4845230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs60812740	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6665930	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6671234	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6674508	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74128893	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7416623	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.85[YRI][hapmap]
rs7535549	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap]
rs7546329	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7548837	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs954744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548532	chr1:189758772-190371671	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917005	chr1:189855484-190259380	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv832104	chr1:189990148-190186708	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2764208	chr1:190123195-190143205	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1003035	chr1:190123195-190291554	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv872755	chr1:190135811-190186387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190138600-190142000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:190138800-190142200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:190140400-190142000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:190140400-190148800	Weak transcription	NH-A	brain
5	chr1:190140400-190149000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:190141800-190142000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:190141800-190142000	Enhancers	Colon Smooth Muscle	Colon
8	chr1:190141800-190142800	Enhancers	Fetal Heart	heart
9	chr1:190141800-190142800	Enhancers	HSMM	muscle
10	chr1:190141800-190142800	Enhancers	HSMMtube	muscle

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