Variant report

Variant	rs4346062
Chromosome Location	chr12:64284283-64284284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:64282867-64284337	A549	lung:	n/a	chr12:64283256-64283265
2	TCF12	chr12:64282875-64284563	A549	lung:	n/a	n/a
3	RUNX3	chr12:64284092-64284336	GM12878	blood:	n/a	chr12:64284228-64284237 chr12:64284228-64284237
4	SP1	chr12:64282953-64284363	A549	lung:	n/a	n/a
5	SP1	chr12:64283015-64284334	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:64283862..64288194-chr12:64291016..64295287,5	MCF-7	breast:
2	chr12:64283993..64286506-chr12:64287434..64289629,2	MCF-7	breast:
3	chr12:64254946..64256892-chr12:64282588..64284962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256399	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17099873	0.95[CHD][hapmap];0.91[TSI][hapmap]
rs17099879	0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs17099886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17099889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099896	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs55884087	0.90[ASN][1000 genomes]
rs61933086	0.90[ASN][1000 genomes]
rs61933093	0.83[ASN][1000 genomes]
rs61933094	0.83[ASN][1000 genomes]
rs61937061	0.98[ASN][1000 genomes]
rs73113977	0.90[ASN][1000 genomes]
rs73126651	0.98[ASN][1000 genomes]
rs73315387	0.90[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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
2	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
3	chr12:64258800-64286200	Weak transcription	Fetal Intestine Small	intestine
4	chr12:64263800-64289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:64264000-64294400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:64274800-64292800	Weak transcription	Right Atrium	heart
7	chr12:64275000-64285000	Weak transcription	Right Ventricle	heart
8	chr12:64276800-64284800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:64277000-64286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:64277000-64291600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:64277200-64285000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:64277200-64285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:64277200-64286200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:64277200-64286400	Weak transcription	Fetal Heart	heart
15	chr12:64277200-64286600	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:64277200-64299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:64277800-64289400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:64278600-64289800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:64279600-64291200	Weak transcription	Fetal Stomach	stomach
20	chr12:64279800-64286400	Weak transcription	Brain Germinal Matrix	brain
21	chr12:64281000-64285200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:64282400-64286400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:64282600-64284600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:64282600-64285000	Enhancers	Fetal Intestine Large	intestine
25	chr12:64283000-64284600	Enhancers	Liver	Liver
26	chr12:64283000-64286600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:64283200-64284800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:64283200-64284800	Weak transcription	Stomach Mucosa	stomach
29	chr12:64283200-64285200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:64283200-64286600	Weak transcription	HSMMtube	muscle
31	chr12:64283200-64286800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:64283200-64298200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:64283200-64298600	Weak transcription	NHEK	skin
34	chr12:64283200-64299000	Weak transcription	HMEC	breast
35	chr12:64283200-64303000	Weak transcription	NHLF	lung
36	chr12:64283200-64312200	Weak transcription	Left Ventricle	heart
37	chr12:64283400-64286400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:64283400-64287000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:64283400-64287000	Weak transcription	Brain Substantia Nigra	brain
40	chr12:64283400-64294400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:64283600-64284600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:64283600-64284600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:64283600-64284800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr12:64283600-64291800	Weak transcription	Brain Anterior Caudate	brain
45	chr12:64283800-64284600	Flanking Active TSS	A549	lung
46	chr12:64283800-64285000	Enhancers	Pancreas	Pancrea
47	chr12:64283800-64286800	Weak transcription	NHDF-Ad	bronchial
48	chr12:64284000-64285000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:64284000-64285600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr12:64284000-64287800	Weak transcription	Osteobl	bone

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