Variant report

Variant	rs256709
Chromosome Location	chr12:31016699-31016700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31007128..31008868-chr12:31015958..31017480,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs192286	0.97[ASN][1000 genomes]
rs192287	0.80[ASN][1000 genomes]
rs2434120	0.98[ASN][1000 genomes]
rs2450097	0.98[ASN][1000 genomes]
rs256706	0.97[ASN][1000 genomes]
rs256707	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs256708	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs256710	0.95[ASN][1000 genomes]
rs256711	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs256712	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs256714	0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs256721	0.81[ASN][1000 genomes]
rs256722	0.81[ASN][1000 genomes]
rs256723	0.81[ASN][1000 genomes]
rs256724	0.81[ASN][1000 genomes]
rs256725	0.81[ASN][1000 genomes]
rs256726	0.81[ASN][1000 genomes]
rs256728	0.81[ASN][1000 genomes]
rs256729	0.80[ASN][1000 genomes]
rs256732	0.81[ASN][1000 genomes]
rs566726	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1052957	chr12:30951520-31191197	Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541439	chr12:30951520-31191197	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1052869	chr12:30951520-31399162	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv2422447	chr12:30954811-31449815	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv832362	chr12:30957786-31124983	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1053711	chr12:30959987-31156297	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv558030	chr12:30969675-31266287	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	esv3377311	chr12:30984179-31044167	Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
12	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs256709	SSBP4	trans	cerebellum	SCAN
rs256709	HIST1H2AC	trans	lymphoblastoid	seeQTL
rs256709	HIST1H2BE	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31015400-31017400	Enhancers	Fetal Heart	heart
2	chr12:31015600-31017200	Enhancers	H9 Cell Line	embryonic stem cell
3	chr12:31016400-31016800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
4	chr12:31016400-31016800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:31016400-31017200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:31016600-31017000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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