Variant report

Variant	rs12309685
Chromosome Location	chr12:124058552-124058553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124056996..124059825-chr12:124068978..124071238,2	MCF-7	breast:
2	chr12:124056030..124058750-chr12:124059393..124062222,4	K562	blood:
3	chr12:124057277..124059073-chr12:124064975..124067218,3	MCF-7	breast:
4	chr12:124056886..124060484-chr12:124067247..124069927,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247373	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10161548	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773023	0.81[EUR][1000 genomes]
rs10773024	0.81[EUR][1000 genomes]
rs10773025	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10846530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846532	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846534	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846536	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846538	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846539	0.81[EUR][1000 genomes]
rs10846542	0.81[EUR][1000 genomes]
rs10846543	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs10846545	0.81[EUR][1000 genomes]
rs11057299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057300	0.81[ASN][1000 genomes]
rs11057301	0.81[ASN][1000 genomes]
rs11057304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057312	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057313	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057322	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057329	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs11057331	0.81[EUR][1000 genomes]
rs11057332	0.81[EUR][1000 genomes]
rs11057336	0.81[EUR][1000 genomes]
rs11572926	0.85[ASN][1000 genomes]
rs11572940	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11572949	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12231444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17840832	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292702	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28403439	1.00[JPT][hapmap]
rs28673982	1.00[JPT][hapmap]
rs34369761	0.81[ASN][1000 genomes]
rs3704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748270	0.87[ASN][1000 genomes]
rs3748271	0.81[EUR][1000 genomes]
rs3850952	0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs3923720	0.87[ASN][1000 genomes]
rs4930713	0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs4930714	0.86[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs61154946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488887	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298287	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[ASN][1000 genomes]
rs7302177	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7303409	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307219	0.81[EUR][1000 genomes]
rs7311689	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316410	0.87[ASN][1000 genomes]
rs73414223	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7358562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967780	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7972380	0.81[ASN][1000 genomes]
rs9919	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124055200-124060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:124055800-124060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:124055800-124060600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124056000-124060800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124056000-124067800	Weak transcription	Lung	lung
13	chr12:124056200-124060600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:124056200-124064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:124056200-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
17	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:124056400-124060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:124056400-124060400	Weak transcription	A549	lung
21	chr12:124056400-124060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:124056400-124065200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:124056400-124065400	Weak transcription	Osteobl	bone
24	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:124056400-124066600	Weak transcription	K562	blood
28	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
31	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
32	chr12:124056800-124066600	Weak transcription	Dnd41	blood
33	chr12:124058000-124058600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:124058400-124058600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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