Variant report

Variant	rs60262639
Chromosome Location	chr12:48203546-48203547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48101224..48103938-chr12:48201884..48203806,2	MCF-7	breast:
2	chr12:48202920..48205906-chr12:48322070..48325166,3	MCF-7	breast:
3	chr12:48185550..48187276-chr12:48201475..48205028,3	K562	blood:
4	chr12:48153014..48156848-chr12:48203481..48206772,3	K562	blood:
5	chr12:48200516..48204856-chr12:48204984..48208825,6	K562	blood:
6	chr12:48196446..48198672-chr12:48203077..48204827,2	K562	blood:

Variant related genes	Relation type
ENSG00000061273	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2525054	1.00[AMR][1000 genomes]
rs2544017	1.00[AMR][1000 genomes]
rs57559473	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58321471	1.00[AMR][1000 genomes]
rs59502643	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	esv999028	chr12:48199301-48209132	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48182000-48206400	Weak transcription	HepG2	liver
2	chr12:48183000-48204000	Weak transcription	Fetal Kidney	kidney
3	chr12:48193400-48205000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:48199400-48206400	Weak transcription	Fetal Brain Female	brain
5	chr12:48199800-48204000	Weak transcription	Aorta	Aorta
6	chr12:48199800-48206800	Enhancers	Spleen	Spleen
7	chr12:48200000-48203600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:48200000-48204800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:48200000-48205800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:48200200-48204200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:48200200-48206600	Enhancers	Lung	lung
12	chr12:48200400-48205400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:48200800-48204200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr12:48200800-48205800	Enhancers	Brain Hippocampus Middle	brain
15	chr12:48201000-48204800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr12:48201000-48206000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:48201000-48206400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:48201000-48206400	Enhancers	Dnd41	blood
19	chr12:48201200-48204600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr12:48201200-48205000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:48201200-48205800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:48201200-48206400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr12:48201200-48206600	Enhancers	Placenta	Placenta
24	chr12:48201400-48204600	Enhancers	HMEC	breast
25	chr12:48201400-48205800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr12:48202000-48204000	Enhancers	Fetal Stomach	stomach
27	chr12:48202000-48204000	Enhancers	NHEK	skin
28	chr12:48202000-48204200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:48202000-48204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:48202400-48204800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr12:48202400-48205000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:48202400-48205400	Weak transcription	Fetal Brain Male	brain
33	chr12:48202400-48206400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:48202400-48208200	Weak transcription	Ovary	ovary
35	chr12:48202600-48204000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:48202600-48204200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:48202600-48205800	Enhancers	Primary B cells from peripheral blood	blood
38	chr12:48202600-48206400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:48202800-48203800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:48202800-48204000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:48202800-48204000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:48202800-48204000	Enhancers	Primary T cells from cord blood	blood
43	chr12:48202800-48204000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:48202800-48204000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:48202800-48204000	Weak transcription	Brain Angular Gyrus	brain
46	chr12:48202800-48204000	Enhancers	Colon Smooth Muscle	Colon
47	chr12:48202800-48204000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr12:48202800-48204400	Weak transcription	Fetal Intestine Large	intestine
49	chr12:48202800-48204600	Weak transcription	Fetal Intestine Small	intestine
50	chr12:48202800-48205200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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