Variant report

Variant	rs12298506
Chromosome Location	chr12:49898355-49898356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49890275..49892320-chr12:49896364..49899114,2	MCF-7	breast:
2	chr12:49897809..49900904-chr12:49903027..49905509,4	MCF-7	breast:
3	chr12:49759716..49761843-chr12:49896903..49899179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11169055	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11830622	1.00[AMR][1000 genomes]
rs11834883	1.00[AMR][1000 genomes]
rs11836969	1.00[AMR][1000 genomes]
rs12296998	1.00[AMR][1000 genomes]
rs12298123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes]
rs12306942	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12309399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311319	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311910	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314348	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320104	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320434	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320612	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12321717	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13377828	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57970210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58867453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59250711	1.00[AMR][1000 genomes]
rs59570650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60254449	1.00[AMR][1000 genomes]
rs60507124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60658484	1.00[AMR][1000 genomes]
rs61227990	0.84[AFR][1000 genomes];1.00[AMR][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	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
3	chr12:49850400-49911000	Weak transcription	K562	blood
4	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
5	chr12:49856800-49898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:49873800-49904600	Weak transcription	Fetal Heart	heart
10	chr12:49874000-49904400	Weak transcription	Fetal Brain Male	brain
11	chr12:49874800-49914200	Weak transcription	Fetal Kidney	kidney
12	chr12:49876400-49911200	Weak transcription	Adipose Nuclei	Adipose
13	chr12:49876800-49905200	Weak transcription	Right Ventricle	heart
14	chr12:49876800-49916200	Weak transcription	Psoas Muscle	Psoas
15	chr12:49877000-49908800	Weak transcription	NHDF-Ad	bronchial
16	chr12:49877000-49909000	Weak transcription	Brain Germinal Matrix	brain
17	chr12:49877600-49902000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:49878600-49918600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:49880400-49916000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:49882200-49918800	Weak transcription	Colonic Mucosa	Colon
21	chr12:49882400-49918400	Weak transcription	Lung	lung
22	chr12:49882600-49916400	Weak transcription	Aorta	Aorta
23	chr12:49884200-49918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:49884200-49918600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:49884400-49899400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:49884600-49916400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:49885600-49901800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:49885800-49904600	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:49886000-49918400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:49886400-49918200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:49889400-49898400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:49890800-49918600	Weak transcription	Brain Anterior Caudate	brain
34	chr12:49890800-49918600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:49891000-49899600	Weak transcription	NHLF	lung
36	chr12:49891000-49916600	Weak transcription	Ovary	ovary
37	chr12:49891200-49900800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:49891200-49904600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:49892200-49899200	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:49893600-49900200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:49893600-49915200	Weak transcription	Placenta	Placenta
42	chr12:49894000-49916600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:49894000-49919600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:49894200-49899600	Weak transcription	HSMM	muscle
45	chr12:49894200-49903000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:49894400-49915000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:49894400-49915400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:49895200-49900000	Weak transcription	Left Ventricle	heart
49	chr12:49895400-49908600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:49895400-49914600	Weak transcription	Duodenum Mucosa	Duodenum

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