Variant report

Variant	rs11680404
Chromosome Location	chr2:48296105-48296106
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	chr2:48132050..48134807-chr2:48295539..48297966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233230	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10495950	0.83[EUR][1000 genomes]
rs11674475	0.86[EUR][1000 genomes]
rs11676381	0.86[EUR][1000 genomes]
rs11677590	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11679956	0.86[EUR][1000 genomes]
rs11680162	0.82[EUR][1000 genomes]
rs11681876	0.83[EUR][1000 genomes]
rs11683689	0.83[EUR][1000 genomes]
rs11687670	0.83[EUR][1000 genomes]
rs11687989	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11689736	0.86[EUR][1000 genomes]
rs11689818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11691493	0.86[EUR][1000 genomes]
rs11692660	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11693267	0.86[EUR][1000 genomes]
rs11695799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11889493	0.88[EUR][1000 genomes]
rs13431982	0.83[EUR][1000 genomes]
rs1586126	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037087	0.92[EUR][1000 genomes]
rs17324473	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17324965	0.87[EUR][1000 genomes]
rs17325048	0.83[EUR][1000 genomes]
rs17396793	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2840147	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34135365	0.86[EUR][1000 genomes]
rs4530419	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs55802119	0.83[EUR][1000 genomes]
rs56037709	0.90[EUR][1000 genomes]
rs58032869	0.95[EUR][1000 genomes]
rs58136909	0.94[EUR][1000 genomes]
rs6730166	0.87[EUR][1000 genomes]
rs6733558	0.87[EUR][1000 genomes]
rs6745620	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6759056	0.88[EUR][1000 genomes]
rs73927905	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73927910	0.91[EUR][1000 genomes]
rs73927911	0.92[EUR][1000 genomes]
rs73927919	0.94[EUR][1000 genomes]
rs7561696	0.99[EUR][1000 genomes]
rs7571905	0.81[EUR][1000 genomes]
rs7581510	0.85[EUR][1000 genomes]
rs7583719	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv833969	chr2:48220927-48328328	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48288600-48303800	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:48293400-48297000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:48294800-48309400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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