Variant report

Variant	rs6746352
Chromosome Location	chr2:149352353-149352354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr2:149351519-149352373	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:149349422..149353491-chr2:149401534..149405104,5	MCF-7	breast:
2	chr2:149351334..149352440-chr2:149364775..149365779,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232238	TF binding region
ENSG00000135999	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1020468	0.96[ASN][1000 genomes]
rs1031290	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10454124	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10928404	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928407	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464036	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12468186	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12472738	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12616115	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12619201	0.96[ASN][1000 genomes]
rs12997473	0.89[EUR][1000 genomes]
rs12997838	0.92[EUR][1000 genomes]
rs13003132	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13004738	0.98[ASN][1000 genomes]
rs13008203	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13010027	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13029692	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16828791	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16828816	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16828836	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16828954	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16828967	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16829006	0.96[ASN][1000 genomes]
rs16829034	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16829057	0.86[JPT][hapmap]
rs1809051	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2382231	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34210886	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34324924	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34671855	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34881950	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35057193	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35076661	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35154707	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35168772	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36067597	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4972285	0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs4972369	0.90[CHB][hapmap]
rs4972375	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972380	0.96[ASN][1000 genomes]
rs4972381	0.96[ASN][1000 genomes]
rs4972383	0.99[ASN][1000 genomes]
rs6430323	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709767	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6743835	0.94[ASN][1000 genomes]
rs6761549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71413623	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs720844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7571333	0.96[ASN][1000 genomes]
rs7578059	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590549	0.96[ASN][1000 genomes]
rs7597133	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606475	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930651	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930652	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1827161	chr2:149352353-149475737	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6746352	NEB	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149350600-149352800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149351600-149352600	Flanking Active TSS	NHEK	skin
3	chr2:149351800-149352400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:149351800-149352800	Enhancers	HMEC	breast
5	chr2:149352000-149352400	Enhancers	Brain Hippocampus Middle	brain
6	chr2:149352000-149357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:149352200-149352400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:149352200-149352600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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