Variant report

Variant	rs923380
Chromosome Location	chr3:119855410-119855411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:119813608..119816143-chr3:119854380..119857222,6	MCF-7	breast:
2	chr3:119851209..119852814-chr3:119855285..119856787,2	MCF-7	breast:
3	chr3:119847191..119849772-chr3:119853713..119855581,2	K562	blood:
4	chr3:119854307..119856524-chr3:119867161..119869039,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NR1I2-1	chr3:119855175-119855628	XLOC_002779
2	lnc-NR1I2-1	chr3:119855175-119855630	ENSG00000242622

No data

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10049256	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10934512	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10934514	0.81[EUR][1000 genomes]
rs10934515	0.86[EUR][1000 genomes]
rs10934516	0.86[EUR][1000 genomes]
rs10934517	0.86[EUR][1000 genomes]
rs1154596	0.87[CEU][hapmap]
rs1154597	0.87[CEU][hapmap]
rs11707711	0.86[EUR][1000 genomes]
rs12152218	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13312998	0.87[CEU][hapmap]
rs1352458	0.86[EUR][1000 genomes]
rs1488761	0.86[EUR][1000 genomes]
rs1488762	0.86[EUR][1000 genomes]
rs1488764	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1492271	0.87[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs16830683	0.87[CEU][hapmap]
rs182839	0.87[CEU][hapmap]
rs1907681	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2035671	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2035672	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2035673	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2035674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2046954	0.80[AMR][1000 genomes]
rs2130000	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2130001	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2171598	0.86[EUR][1000 genomes]
rs2171599	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2319541	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2319542	0.86[EUR][1000 genomes]
rs2319543	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs28398784	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874022	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2874023	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3112282	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3112283	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs334534	0.87[CEU][hapmap]
rs334539	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334540	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs334545	0.81[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334549	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs334561	0.87[CEU][hapmap]
rs4488869	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4676804	0.86[EUR][1000 genomes]
rs4676809	0.86[EUR][1000 genomes]
rs4676822	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4676832	0.82[EUR][1000 genomes]
rs6438554	0.87[CEU][hapmap]
rs6438558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438559	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6438561	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6438562	0.84[EUR][1000 genomes]
rs6438564	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438566	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438567	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6764549	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6769988	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6776122	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6777971	0.82[EUR][1000 genomes]
rs6781470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782570	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6784239	0.87[CEU][hapmap]
rs6785050	0.87[CEU][hapmap]
rs6794478	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6797689	0.87[CEU][hapmap]
rs6803611	0.87[CEU][hapmap]
rs6805050	0.86[EUR][1000 genomes]
rs6807868	0.87[CEU][hapmap]
rs7637828	0.86[EUR][1000 genomes]
rs7641838	0.86[EUR][1000 genomes]
rs7642171	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7644268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650554	0.87[CEU][hapmap]
rs7653263	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7653396	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs787211	0.87[CEU][hapmap]
rs901920	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902790	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs902791	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs902792	0.86[EUR][1000 genomes]
rs902794	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs902795	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs923726	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs923727	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs923728	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs9289142	0.86[EUR][1000 genomes]
rs9289143	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs979682	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs9813834	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9841122	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9841303	1.00[CHB][hapmap]
rs9842302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs9849023	0.81[EUR][1000 genomes]
rs9853082	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9857123	0.86[EUR][1000 genomes]
rs9858566	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9868058	0.83[EUR][1000 genomes]
rs9868312	0.86[EUR][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119836800-119860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:119844200-119863400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:119851400-119856400	Weak transcription	Pancreas	Pancrea
4	chr3:119854200-119856000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:119854400-119855800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:119854400-119863200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:119854600-119863000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:119854800-119855800	Weak transcription	HMEC	breast
9	chr3:119854800-119860800	Weak transcription	Hela-S3	cervix
10	chr3:119855000-119862600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:119855200-119856400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:119855400-119856600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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