Variant report

Variant	rs17840860
Chromosome Location	chr12:83043909-83043910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:83042670..83045643-chr12:83080310..83082308,2	MCF-7	breast:
2	chr12:83038079..83039947-chr12:83043283..83045373,2	MCF-7	breast:
3	chr12:83042183..83044298-chr12:83079732..83081351,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10506877	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12423462	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12423777	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12424179	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12424928	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12427053	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12578874	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17722140	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17722367	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17778686	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1882582	1.00[GIH][hapmap]
rs1922578	0.86[JPT][hapmap]
rs4882519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4882520	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.95[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	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv519197	chr12:82831845-83056476	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1053649	chr12:82893253-83054109	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv983443	chr12:83020399-83048001	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83039800-83044200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:83040000-83044200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:83040000-83044200	Weak transcription	NHEK	skin
4	chr12:83042400-83044200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:83042400-83044400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:83042600-83044200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:83042600-83044200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:83042600-83044400	Weak transcription	Brain Angular Gyrus	brain
9	chr12:83042600-83044400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:83042600-83044400	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:83042600-83044400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:83042600-83045200	Enhancers	GM12878-XiMat	blood
13	chr12:83042800-83044200	Weak transcription	Brain Anterior Caudate	brain
14	chr12:83042800-83044400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:83043400-83044000	Enhancers	Stomach Mucosa	stomach
16	chr12:83043600-83044200	Weak transcription	Gastric	stomach
17	chr12:83043600-83046200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:83043600-83046200	Enhancers	HMEC	breast
19	chr12:83043800-83044400	Enhancers	A549	lung
20	chr12:83043800-83046200	Enhancers	Hela-S3	cervix

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