Variant report

Variant	rs1259882
Chromosome Location	chr12:32097629-32097630
allele	A/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	RAD21	chr12:32097504-32097923	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr12:32097573-32097794	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32096850..32099855-chr12:32103347..32105701,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242314	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11051695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151000	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151001	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151003	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151004	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1151006	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259881	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1666252	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16919099	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7980973	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	33 gene(s)	inside rSNPs	diseases
4	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
10	nsv1040680	chr12:32079034-32124694	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1259882	FAM60A	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32080600-32111400	Weak transcription	Aorta	Aorta
2	chr12:32093000-32098000	ZNF genes & repeats	Dnd41	blood
3	chr12:32093000-32111200	Weak transcription	Psoas Muscle	Psoas
4	chr12:32093400-32100200	Weak transcription	Adipose Nuclei	Adipose
5	chr12:32094800-32098000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr12:32095000-32098200	Weak transcription	A549	lung
7	chr12:32095400-32097800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr12:32095800-32097800	Strong transcription	Liver	Liver
9	chr12:32095800-32098200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:32096000-32098200	Weak transcription	Left Ventricle	heart
11	chr12:32096400-32098000	ZNF genes & repeats	Thymus	Thymus
12	chr12:32097000-32097800	Enhancers	NHEK	skin
13	chr12:32097400-32097800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:32097400-32097800	ZNF genes & repeats	Lung	lung
15	chr12:32097400-32097800	ZNF genes & repeats	Ovary	ovary
16	chr12:32097400-32097800	Enhancers	HMEC	breast
17	chr12:32097400-32098000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:32097400-32098000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr12:32097400-32098000	ZNF genes & repeats	Fetal Stomach	stomach
20	chr12:32097600-32098000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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