Variant report

Variant	rs12227642
Chromosome Location	chr12:39804421-39804422
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	chr12:39803978..39806554-chr12:39812297..39814697,2	MCF-7	breast:
2	chr12:39804413..39806857-chr12:39807005..39809707,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11171568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11171662	0.83[ASN][1000 genomes]
rs11171666	0.82[ASN][1000 genomes]
rs11171669	0.87[ASN][1000 genomes]
rs11171682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11171691	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11171732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs11171786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs11171794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs11171797	0.86[ASN][1000 genomes]
rs11171834	0.86[ASN][1000 genomes]
rs11171844	0.86[ASN][1000 genomes]
rs11171857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11171940	0.88[ASN][1000 genomes]
rs11171949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs11171955	0.88[ASN][1000 genomes]
rs11171957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs11172024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11172035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs11172082	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172109	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11172168	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172175	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172204	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172263	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172347	0.86[EUR][1000 genomes]
rs11172359	0.86[EUR][1000 genomes]
rs11172373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11172471	0.86[EUR][1000 genomes]
rs11172474	0.86[EUR][1000 genomes]
rs11172502	0.86[EUR][1000 genomes]
rs11172566	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11172603	0.83[EUR][1000 genomes]
rs11172696	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap]
rs11172702	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap]
rs11543371	0.86[EUR][1000 genomes]
rs12227092	0.86[EUR][1000 genomes]
rs12228285	0.86[EUR][1000 genomes]
rs12228664	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12231250	0.88[ASN][1000 genomes]
rs12231735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs17127036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs17127115	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17127119	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4595585	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs56154721	0.86[ASN][1000 genomes]
rs56326136	0.86[ASN][1000 genomes]
rs56885420	0.80[ASN][1000 genomes]
rs57785083	0.88[ASN][1000 genomes]
rs58125663	0.86[ASN][1000 genomes]
rs58648215	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59380486	0.86[EUR][1000 genomes]
rs60505849	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61101304	0.84[ASN][1000 genomes]
rs61453715	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308295	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs7964039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs9788260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
2	chr12:39785000-39829200	Weak transcription	K562	blood
3	chr12:39790000-39816200	Weak transcription	Right Ventricle	heart
4	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
5	chr12:39795400-39816600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:39796200-39805600	Weak transcription	Liver	Liver
7	chr12:39797600-39805400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:39797600-39812000	Weak transcription	HMEC	breast
9	chr12:39798200-39807000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:39798200-39809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:39800800-39806000	Weak transcription	Placenta	Placenta
12	chr12:39800800-39807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:39800800-39807400	Weak transcription	GM12878-XiMat	blood
14	chr12:39800800-39807800	Weak transcription	Ovary	ovary
15	chr12:39800800-39812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:39800800-39814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:39801000-39804800	Weak transcription	Fetal Brain Female	brain
18	chr12:39801000-39805200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:39801000-39807200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:39801000-39808000	Weak transcription	Brain Anterior Caudate	brain
21	chr12:39801000-39815800	Weak transcription	Psoas Muscle	Psoas
22	chr12:39801200-39808200	Weak transcription	A549	lung
23	chr12:39801400-39807000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:39801400-39807400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:39801600-39811000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:39802000-39811800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:39802200-39805200	Weak transcription	Brain Germinal Matrix	brain
28	chr12:39802400-39809200	Weak transcription	Left Ventricle	heart
29	chr12:39802400-39816000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:39802800-39806800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:39803000-39805000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:39803400-39807200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:39803800-39805000	Enhancers	Fetal Heart	heart
34	chr12:39803800-39805800	Weak transcription	Fetal Intestine Small	intestine
35	chr12:39803800-39806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:39804000-39808200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:39804000-39811800	Weak transcription	Adipose Nuclei	Adipose
38	chr12:39804400-39809000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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