Variant report

Variant	rs12299097
Chromosome Location	chr12:67666721-67666722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:67639415..67642144-chr12:67665487..67667188,2	MCF-7	breast:
2	chr12:67665523..67668331-chr12:67690936..67692642,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10128823	1.00[EUR][1000 genomes]
rs10129028	1.00[EUR][1000 genomes]
rs11176669	0.88[AFR][1000 genomes]
rs11176670	0.94[AFR][1000 genomes]
rs11176672	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176676	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11176679	1.00[EUR][1000 genomes]
rs11176684	1.00[EUR][1000 genomes]
rs11176691	1.00[EUR][1000 genomes]
rs11176692	1.00[EUR][1000 genomes]
rs11176693	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11176694	1.00[EUR][1000 genomes]
rs11176715	1.00[EUR][1000 genomes]
rs11176740	1.00[EUR][1000 genomes]
rs11503726	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12297966	1.00[EUR][1000 genomes]
rs12299042	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12300582	1.00[EUR][1000 genomes]
rs12303089	1.00[EUR][1000 genomes]
rs12305377	0.95[AFR][1000 genomes]
rs12306375	1.00[EUR][1000 genomes]
rs12306657	0.94[AFR][1000 genomes]
rs12307363	1.00[EUR][1000 genomes]
rs12307464	1.00[EUR][1000 genomes]
rs12311491	1.00[EUR][1000 genomes]
rs12311797	1.00[EUR][1000 genomes]
rs12311840	1.00[EUR][1000 genomes]
rs12311845	1.00[EUR][1000 genomes]
rs12312040	1.00[EUR][1000 genomes]
rs12313282	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12314503	1.00[EUR][1000 genomes]
rs12315624	1.00[EUR][1000 genomes]
rs12318518	1.00[EUR][1000 genomes]
rs12318591	1.00[EUR][1000 genomes]
rs12318995	1.00[EUR][1000 genomes]
rs12320566	1.00[EUR][1000 genomes]
rs12321396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12322901	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17103392	1.00[EUR][1000 genomes]
rs17103652	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17103772	1.00[EUR][1000 genomes]
rs17120707	1.00[EUR][1000 genomes]
rs17120710	1.00[EUR][1000 genomes]
rs3087577	0.87[AFR][1000 genomes]
rs4083304	1.00[EUR][1000 genomes]
rs57886620	1.00[EUR][1000 genomes]
rs61281993	0.87[AFR][1000 genomes]
rs61504642	1.00[EUR][1000 genomes]
rs6581751	1.00[EUR][1000 genomes]
rs7135195	1.00[EUR][1000 genomes]
rs7294827	1.00[EUR][1000 genomes]
rs7306853	1.00[EUR][1000 genomes]
rs7307643	1.00[EUR][1000 genomes]
rs7312079	1.00[EUR][1000 genomes]
rs73320752	1.00[EUR][1000 genomes]
rs73322616	1.00[EUR][1000 genomes]
rs73326445	1.00[EUR][1000 genomes]
rs73326448	1.00[EUR][1000 genomes]
rs73326466	1.00[EUR][1000 genomes]
rs7954050	0.89[AFR][1000 genomes]
rs7954999	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7962872	1.00[EUR][1000 genomes]
rs7964763	1.00[EUR][1000 genomes]
rs7966031	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977574	1.00[EUR][1000 genomes]
rs9989007	1.00[EUR][1000 genomes]
rs9989023	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67664400-67666800	Enhancers	Brain Substantia Nigra	brain
2	chr12:67664400-67669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:67664400-67669200	Weak transcription	Gastric	stomach
4	chr12:67664400-67669400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:67664600-67684000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:67664800-67666800	Enhancers	Primary B cells from cord blood	blood
7	chr12:67664800-67694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:67664800-67699600	Weak transcription	Aorta	Aorta
9	chr12:67665200-67666800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:67665200-67666800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:67665200-67666800	Enhancers	Adipose Nuclei	Adipose
12	chr12:67665200-67666800	Enhancers	Fetal Heart	heart
13	chr12:67665200-67667000	Weak transcription	Fetal Thymus	thymus
14	chr12:67665200-67667200	Enhancers	Rectal Smooth Muscle	rectum
15	chr12:67665200-67667400	Weak transcription	Stomach Mucosa	stomach
16	chr12:67665200-67667800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:67665200-67668000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:67665200-67668600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:67665200-67669000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:67665200-67669400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:67665200-67670600	Weak transcription	Brain Angular Gyrus	brain
22	chr12:67665200-67671200	Weak transcription	Right Atrium	heart
23	chr12:67665200-67671800	Weak transcription	Esophagus	oesophagus
24	chr12:67665200-67673000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:67665200-67675400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:67665200-67675800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:67665200-67675800	Weak transcription	Placenta	Placenta
28	chr12:67665200-67675800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:67665200-67676200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:67665200-67678400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:67665200-67684400	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:67665200-67684600	Weak transcription	Thymus	Thymus
33	chr12:67665200-67690200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:67665200-67699000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:67665400-67667200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:67665400-67668200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr12:67665400-67669600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:67665400-67670200	Weak transcription	HSMMtube	muscle
39	chr12:67665400-67671200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:67665400-67687600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:67665600-67667200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:67665600-67667200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:67665600-67667800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:67665600-67668000	Enhancers	Duodenum Mucosa	Duodenum
45	chr12:67665600-67668200	Enhancers	Primary T cells from cord blood	blood
46	chr12:67665600-67668200	Enhancers	NHEK	skin
47	chr12:67665600-67669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:67665600-67672000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:67665600-67672000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr12:67665600-67673800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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