Variant report

Variant	rs17099873
Chromosome Location	chr12:64240002-64240003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64239389..64242178-chr12:64352043..64353568,2	MCF-7	breast:
2	chr12:64233673..64240233-chr12:64613167..64618011,13	MCF-7	breast:
3	chr12:64238988..64240941-chr12:64313933..64315670,2	MCF-7	breast:
4	chr12:64238646..64240219-chr12:64329765..64332123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174206	Chromatin interaction
ENSG00000243024	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11837218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17099872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099879	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17099886	0.95[CHD][hapmap]
rs17099889	0.95[CHD][hapmap]
rs17099893	0.95[CHD][hapmap];0.91[TSI][hapmap]
rs4346062	0.95[CHD][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	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
7	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
8	esv1797043	chr12:64237504-64256568	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
9	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64236800-64240200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:64236800-64240800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:64237000-64240200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:64237000-64240200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr12:64237000-64240200	Active TSS	A549	lung
6	chr12:64237000-64240200	Active TSS	HSMMtube	muscle
7	chr12:64237000-64240200	Active TSS	NHLF	lung
8	chr12:64237000-64240400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr12:64237000-64240400	Active TSS	Brain Anterior Caudate	brain
10	chr12:64237000-64240400	Active TSS	Pancreas	Pancrea
11	chr12:64237000-64240400	Active TSS	HSMM	muscle
12	chr12:64237000-64240600	Active TSS	Psoas Muscle	Psoas
13	chr12:64237200-64240200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:64237200-64240200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:64237200-64240200	Active TSS	NHEK	skin
16	chr12:64237200-64240400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:64237200-64240400	Active TSS	NHDF-Ad	bronchial
18	chr12:64237400-64240200	Active TSS	Brain Angular Gyrus	brain
19	chr12:64237600-64240200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:64237800-64240400	Active TSS	Fetal Brain Male	brain
21	chr12:64237800-64240800	Active TSS	Colonic Mucosa	Colon
22	chr12:64238800-64240800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr12:64239000-64240400	Active TSS	Brain Germinal Matrix	brain
24	chr12:64239000-64240400	Weak transcription	Lung	lung
25	chr12:64239000-64240400	Weak transcription	Small Intestine	intestine
26	chr12:64239000-64240600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:64239200-64240400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:64239200-64240400	Active TSS	Fetal Brain Female	brain
29	chr12:64239400-64240200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr12:64239400-64240200	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr12:64239400-64240200	Flanking Active TSS	Fetal Heart	heart
32	chr12:64239400-64240400	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:64239400-64240600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:64239400-64241000	Enhancers	Liver	Liver
35	chr12:64239400-64242000	Weak transcription	Placenta	Placenta
36	chr12:64239600-64240200	Enhancers	Aorta	Aorta
37	chr12:64239600-64240200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr12:64239600-64240400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:64239600-64240400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr12:64239600-64240600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:64239600-64240600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:64239600-64240600	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr12:64239600-64240600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr12:64239600-64240600	Flanking Active TSS	HepG2	liver
45	chr12:64239600-64240600	Flanking Active TSS	HUVEC	blood vessel
46	chr12:64239600-64240600	Flanking Active TSS	NH-A	brain
47	chr12:64239600-64240800	Flanking Active TSS	Fetal Kidney	kidney
48	chr12:64239800-64240200	Enhancers	H1 Cell Line	embryonic stem cell
49	chr12:64239800-64240200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:64239800-64240200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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