Variant report

Variant	rs57260154
Chromosome Location	chr12:42749929-42749930
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42749730..42752299-chr12:42753971..42755536,2	MCF-7	breast:
2	chr12:42539891..42542441-chr12:42748681..42750572,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11385212	0.83[AMR][1000 genomes]
rs1234113	0.83[AMR][1000 genomes]
rs1683193	0.83[AMR][1000 genomes]
rs2639128	0.83[AMR][1000 genomes]
rs57166587	1.00[AMR][1000 genomes]
rs57549495	0.83[AMR][1000 genomes]
rs57582332	0.83[AMR][1000 genomes]
rs58488818	1.00[AMR][1000 genomes]
rs58902406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59321446	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60341977	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs712113	0.83[AMR][1000 genomes]
rs712117	0.83[AMR][1000 genomes]
rs712121	0.83[AMR][1000 genomes]
rs712128	0.83[AMR][1000 genomes]
rs7136339	1.00[AMR][1000 genomes]
rs7303532	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73270272	0.83[AMR][1000 genomes]
rs73272006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73272039	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73272041	1.00[AMR][1000 genomes]
rs73272052	1.00[AMR][1000 genomes]
rs73272054	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73272065	1.00[AMR][1000 genomes]
rs73273905	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73273908	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73273915	1.00[AMR][1000 genomes]
rs73273940	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73273948	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73281848	0.83[AMR][1000 genomes]
rs73281857	0.83[AMR][1000 genomes]
rs73281868	0.83[AMR][1000 genomes]
rs73281890	0.83[AMR][1000 genomes]
rs73281897	0.83[AMR][1000 genomes]
rs73283726	0.83[AMR][1000 genomes]
rs73283728	0.83[AMR][1000 genomes]
rs73283731	0.83[AMR][1000 genomes]
rs73283737	0.83[AMR][1000 genomes]
rs73283752	0.83[AMR][1000 genomes]
rs73283757	0.83[AMR][1000 genomes]
rs73283764	0.83[AMR][1000 genomes]
rs73283782	1.00[AMR][1000 genomes]
rs73285606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285610	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74078990	1.00[AMR][1000 genomes]
rs7957401	0.83[AMR][1000 genomes]
rs7960285	0.83[AMR][1000 genomes]
rs7964994	0.83[AMR][1000 genomes]
rs850828	0.83[AMR][1000 genomes]
rs864291	0.83[AMR][1000 genomes]
rs864298	0.83[AMR][1000 genomes]
rs9669751	0.83[AMR][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	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721000-42758000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:42721600-42750000	Weak transcription	Aorta	Aorta
4	chr12:42721600-42750600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:42721600-42751800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:42721600-42769000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:42721600-42778600	Weak transcription	Spleen	Spleen
8	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
9	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:42721800-42750200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:42721800-42756200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:42721800-42769600	Weak transcription	Brain Substantia Nigra	brain
13	chr12:42721800-42769800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:42721800-42797000	Weak transcription	NHLF	lung
15	chr12:42721800-42803600	Weak transcription	Gastric	stomach
16	chr12:42722000-42769600	Weak transcription	Brain Anterior Caudate	brain
17	chr12:42722000-42769600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:42722000-42772600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
20	chr12:42722200-42750200	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:42722200-42752800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:42722200-42769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:42724400-42755400	Weak transcription	Pancreas	Pancrea
24	chr12:42730400-42750000	Weak transcription	Ovary	ovary
25	chr12:42730600-42750000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:42730800-42769600	Weak transcription	NH-A	brain
27	chr12:42731000-42757400	Weak transcription	Brain Germinal Matrix	brain
28	chr12:42731000-42768800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:42731200-42754000	Weak transcription	HUVEC	blood vessel
30	chr12:42731400-42769600	Weak transcription	Fetal Lung	lung
31	chr12:42731800-42770400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:42732000-42754200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:42732000-42754200	Weak transcription	Lung	lung
34	chr12:42732200-42781200	Weak transcription	Fetal Brain Female	brain
35	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:42732400-42763600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:42732400-42769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:42732600-42750000	Weak transcription	Right Ventricle	heart
39	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:42738000-42754000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:42738000-42787400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr12:42742000-42758400	Weak transcription	Stomach Mucosa	stomach
44	chr12:42742600-42758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:42743000-42755000	Weak transcription	Brain Angular Gyrus	brain
46	chr12:42743200-42755600	Weak transcription	NHEK	skin
47	chr12:42745000-42750400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:42745000-42751800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr12:42745000-42753000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:42745000-42753400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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