Variant report

Variant	rs2999535
Chromosome Location	chr1:151978287-151978288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151978082..151980284-chr1:152020227..152021927,2	MCF-7	breast:
2	chr1:151906723..151908280-chr1:151976802..151979658,2	MCF-7	breast:
3	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
4	chr1:151978047..151980074-chr1:152004028..152006807,2	K562	blood:
5	chr1:151879750..151883668-chr1:151974501..151979582,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs10158030	1.00[CHB][hapmap]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888453	1.00[CHB][hapmap]
rs11204911	1.00[CHB][hapmap];0.88[MEX][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1387835	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1490187	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs1490188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490191	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs1496037	1.00[CHB][hapmap]
rs1552606	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs1552607	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1602252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1602254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17583707	1.00[CHB][hapmap]
rs1873311	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1873312	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs1967084	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1967085	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979638	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2338018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932563	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932572	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999514	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999527	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999529	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2999536	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999537	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999538	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999551	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2999558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3007676	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3007679	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs3007690	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs3007700	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3007701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3007704	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3007713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3122300	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3122301	1.00[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs3134814	1.00[CHB][hapmap]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs6587629	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs6587630	1.00[CHB][hapmap]
rs6587641	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659029	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6685291	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs6691350	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs6704157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7529451	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs7532721	1.00[CHB][hapmap]
rs882099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902314	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9943225	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs994974	1.00[AMR][1000 genomes];1.00[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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151976000-151978400	Enhancers	Right Ventricle	heart
2	chr1:151976600-151979400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:151976600-151979400	Weak transcription	HMEC	breast
4	chr1:151976800-151993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:151977000-151979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:151977000-151986000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:151977200-151978400	Bivalent Enhancer	Fetal Heart	heart
8	chr1:151977200-151979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:151978200-151979000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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