Variant report

Variant	rs6542841
Chromosome Location	chr2:99489039-99489040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99480402..99483118-chr2:99488254..99491122,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10169003	0.92[AFR][1000 genomes]
rs10175560	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10192266	0.81[EUR][1000 genomes]
rs11123756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11887536	0.84[AFR][1000 genomes]
rs11900176	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11900524	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12467504	0.84[EUR][1000 genomes]
rs12474283	0.81[CEU][hapmap]
rs12478574	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12712033	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs12712034	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs12712037	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712039	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12712040	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12712042	0.81[EUR][1000 genomes]
rs12990579	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004700	0.81[CEU][hapmap]
rs13004923	0.93[AFR][1000 genomes]
rs13005124	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs13005148	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006398	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13024838	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13028500	0.92[CEU][hapmap]
rs1581249	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17758170	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes]
rs1878589	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1949424	0.91[EUR][1000 genomes]
rs1962029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4311103	0.88[CEU][hapmap]
rs4499468	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4553869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4850890	0.81[EUR][1000 genomes]
rs4851174	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs4851175	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4851176	0.81[EUR][1000 genomes]
rs6542845	0.81[EUR][1000 genomes]
rs6704682	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6724477	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6739097	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs6741166	0.92[EUR][1000 genomes]
rs6742047	0.81[EUR][1000 genomes]
rs6752025	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6757098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7423519	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7565510	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7565614	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7565736	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7565819	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7588441	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7590596	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7593332	0.91[EUR][1000 genomes]
rs7608889	0.82[CEU][hapmap]
rs883773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs925887	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
3	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:99486400-99489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:99486600-99489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:99486600-99489800	Weak transcription	NHEK	skin
7	chr2:99486800-99489600	Weak transcription	Placenta	Placenta
8	chr2:99486800-99491000	Weak transcription	GM12878-XiMat	blood
9	chr2:99487000-99489600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:99487000-99489600	Weak transcription	HMEC	breast
11	chr2:99487600-99499400	Weak transcription	Gastric	stomach
12	chr2:99488000-99489600	Weak transcription	Esophagus	oesophagus
13	chr2:99488200-99497200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:99489000-99489600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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