Variant report

Variant	rs17127119
Chromosome Location	chr12:39820232-39820233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39819480..39821509-chr12:39835676..39837494,3	MCF-7	breast:
2	chr12:39810025..39813517-chr12:39819590..39821395,3	MCF-7	breast:
3	chr12:39819486..39821457-chr12:39836641..39838666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11171568	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11171669	0.81[ASN][1000 genomes]
rs11171682	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11171691	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11171732	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs11171786	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs11171794	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs11171857	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11171940	0.82[ASN][1000 genomes]
rs11171949	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs11171955	0.82[ASN][1000 genomes]
rs11171957	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs11172024	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11172035	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs11172082	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172105	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172109	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172168	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172175	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172204	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172263	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172347	0.85[EUR][1000 genomes]
rs11172359	0.85[EUR][1000 genomes]
rs11172373	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11172471	0.85[EUR][1000 genomes]
rs11172474	0.85[EUR][1000 genomes]
rs11172502	0.85[EUR][1000 genomes]
rs11172566	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs11172603	0.81[EUR][1000 genomes]
rs11172696	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs11172702	0.84[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs11543371	0.85[EUR][1000 genomes]
rs12227092	0.85[EUR][1000 genomes]
rs12227642	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]
rs12228285	0.85[EUR][1000 genomes]
rs12228664	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12231250	0.82[ASN][1000 genomes]
rs12231735	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs17127036	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs17127115	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595585	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs57785083	0.82[ASN][1000 genomes]
rs58648215	0.81[ASN][1000 genomes]
rs59380486	0.85[EUR][1000 genomes]
rs60505849	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61453715	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7308295	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs7964039	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs9788260	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39785000-39829200	Weak transcription	K562	blood
2	chr12:39794200-39824800	Weak transcription	Right Atrium	heart
3	chr12:39806600-39834200	Weak transcription	Hela-S3	cervix
4	chr12:39808600-39821600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:39808600-39830800	Weak transcription	Fetal Brain Female	brain
6	chr12:39810000-39821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39813600-39833400	Weak transcription	Brain Germinal Matrix	brain
8	chr12:39814200-39821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39814200-39821400	Weak transcription	Placenta	Placenta
10	chr12:39814200-39825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:39814400-39833800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:39814800-39820800	Weak transcription	A549	lung
13	chr12:39816000-39834000	Weak transcription	Left Ventricle	heart
14	chr12:39817400-39824600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39817400-39824600	Weak transcription	Right Ventricle	heart
16	chr12:39818400-39823200	Weak transcription	Fetal Heart	heart
17	chr12:39819000-39822800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:39819000-39824600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:39820000-39820400	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr12:39820000-39822400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:39820200-39822600	Enhancers	HMEC	breast
22	chr12:39820200-39824000	Enhancers	HepG2	liver

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