Variant report

Variant	rs60658484
Chromosome Location	chr12:49876641-49876642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49875150..49877752-chr12:49892252..49894698,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11169055	1.00[AMR][1000 genomes]
rs11830622	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11836969	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12296998	1.00[AMR][1000 genomes]
rs12298123	1.00[AMR][1000 genomes]
rs12298506	1.00[AMR][1000 genomes]
rs12300085	1.00[AMR][1000 genomes]
rs12306942	1.00[AMR][1000 genomes]
rs12309399	1.00[AMR][1000 genomes]
rs12310046	1.00[AMR][1000 genomes]
rs12311319	1.00[AMR][1000 genomes]
rs12311910	1.00[AMR][1000 genomes]
rs12313583	1.00[AMR][1000 genomes]
rs12314348	1.00[AMR][1000 genomes]
rs12315746	1.00[AMR][1000 genomes]
rs12315941	1.00[AMR][1000 genomes]
rs12318913	1.00[AMR][1000 genomes]
rs12320104	1.00[AMR][1000 genomes]
rs12320434	1.00[AMR][1000 genomes]
rs12320612	1.00[AMR][1000 genomes]
rs12321717	1.00[AMR][1000 genomes]
rs13377828	1.00[AMR][1000 genomes]
rs57970210	1.00[AMR][1000 genomes]
rs58867453	1.00[AMR][1000 genomes]
rs59250711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59570650	1.00[AMR][1000 genomes]
rs60254449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60507124	1.00[AMR][1000 genomes]
rs61122194	0.86[AFR][1000 genomes]
rs61227990	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:97 , 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	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
4	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:49850400-49878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:49850400-49911000	Weak transcription	K562	blood
7	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
8	chr12:49854400-49878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:49856400-49883400	Weak transcription	Brain Anterior Caudate	brain
10	chr12:49856600-49890200	Weak transcription	Primary T cells from cord blood	blood
11	chr12:49856600-49890200	Weak transcription	Ovary	ovary
12	chr12:49856800-49883600	Weak transcription	Dnd41	blood
13	chr12:49856800-49898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:49859400-49883400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:49859400-49888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:49869600-49890000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:49870000-49877600	Weak transcription	GM12878-XiMat	blood
19	chr12:49870200-49884600	Weak transcription	Spleen	Spleen
20	chr12:49870400-49877600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49870600-49878200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:49870600-49878400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:49870600-49878800	Weak transcription	Fetal Stomach	stomach
24	chr12:49871400-49878800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:49872200-49895000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:49873000-49881000	Weak transcription	Lung	lung
27	chr12:49873000-49890400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:49873400-49879000	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:49873600-49878600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:49873800-49904600	Weak transcription	Fetal Heart	heart
33	chr12:49874000-49889800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:49874000-49904400	Weak transcription	Fetal Brain Male	brain
35	chr12:49874200-49890600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:49874800-49914200	Weak transcription	Fetal Kidney	kidney
37	chr12:49875200-49878400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:49875400-49876800	Enhancers	HUVEC	blood vessel
39	chr12:49875400-49878000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:49875800-49876800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:49875800-49876800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:49875800-49877000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:49875800-49877200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr12:49875800-49877200	Enhancers	HepG2	liver
45	chr12:49875800-49878000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:49875800-49878000	Enhancers	Hela-S3	cervix
47	chr12:49875800-49878000	Enhancers	HMEC	breast
48	chr12:49875800-49878000	Enhancers	NHEK	skin
49	chr12:49875800-49878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:49875800-49878600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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