Variant report

Variant	rs12231250
Chromosome Location	chr12:39795128-39795129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39793686..39797447-chr12:39835348..39837306,4	MCF-7	breast:
2	chr12:39792518..39795193-chr12:39798527..39801393,2	K562	blood:
3	chr12:39793372..39796238-chr12:39806830..39809770,2	K562	blood:
4	chr12:39788415..39791571-chr12:39793998..39797026,3	K562	blood:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11171568	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11171682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171691	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171786	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171794	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171797	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171844	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171857	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172109	0.92[AFR][1000 genomes]
rs11172168	0.82[ASN][1000 genomes]
rs11172175	0.82[ASN][1000 genomes]
rs11172204	0.82[ASN][1000 genomes]
rs11172263	0.83[EUR][1000 genomes]
rs12227642	0.88[ASN][1000 genomes]
rs12228664	0.83[EUR][1000 genomes]
rs12231735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17127036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17127059	0.92[AFR][1000 genomes]
rs17127072	0.92[AFR][1000 genomes]
rs17127115	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs17127119	0.82[ASN][1000 genomes]
rs56154721	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56326136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56885420	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57785083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58125663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58648215	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61101304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61453715	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7964039	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788260	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39781400-39800200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:39782200-39796800	Weak transcription	A549	lung
4	chr12:39785000-39796800	Weak transcription	HMEC	breast
5	chr12:39785000-39829200	Weak transcription	K562	blood
6	chr12:39785200-39796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39785400-39796600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:39786400-39796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39789000-39799400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:39789200-39800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:39789400-39795400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
13	chr12:39791800-39796200	Weak transcription	Left Ventricle	heart
14	chr12:39791800-39797800	Enhancers	Fetal Heart	heart
15	chr12:39791800-39799600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:39792000-39796800	Weak transcription	GM12878-XiMat	blood
17	chr12:39792600-39798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:39793600-39799800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:39794200-39795400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:39794200-39795400	Weak transcription	NHEK	skin
21	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
22	chr12:39795000-39795400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:39795000-39795800	Enhancers	Colon Smooth Muscle	Colon
24	chr12:39795000-39796200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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