Variant report

Variant	rs28969463
Chromosome Location	chr12:121568371-121568372
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121566738..121568870-chr12:121570376..121572315,2	MCF-7	breast:
2	chr12:121562465..121564050-chr12:121566966..121568974,2	MCF-7	breast:
3	chr12:121566845..121568445-chr12:121570737..121572613,2	K562	blood:
4	chr12:121550877..121553101-chr12:121566808..121569789,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089041	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10492051	0.85[EUR][1000 genomes]
rs1180008	0.88[EUR][1000 genomes]
rs17433716	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17434682	0.95[EUR][1000 genomes]
rs17434731	0.95[EUR][1000 genomes]
rs17434809	0.95[EUR][1000 genomes]
rs17512249	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17525767	0.94[EUR][1000 genomes]
rs17526121	0.81[EUR][1000 genomes]
rs1796415	0.84[EUR][1000 genomes]
rs208291	0.94[EUR][1000 genomes]
rs28360439	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3850517	0.82[EUR][1000 genomes]
rs4083358	0.82[EUR][1000 genomes]
rs41416850	0.88[EUR][1000 genomes]
rs4445718	0.82[EUR][1000 genomes]
rs55814439	0.92[EUR][1000 genomes]
rs55817936	0.87[EUR][1000 genomes]
rs55847639	0.81[EUR][1000 genomes]
rs56017922	0.95[EUR][1000 genomes]
rs560422	0.95[EUR][1000 genomes]
rs56156773	0.88[EUR][1000 genomes]
rs56159890	0.92[EUR][1000 genomes]
rs7312738	0.88[EUR][1000 genomes]
rs73214193	0.81[EUR][1000 genomes]
rs73214200	0.82[EUR][1000 genomes]
rs73214202	0.81[EUR][1000 genomes]
rs73216105	0.82[EUR][1000 genomes]
rs73216108	0.84[EUR][1000 genomes]
rs73216109	0.88[EUR][1000 genomes]
rs73216110	0.88[EUR][1000 genomes]
rs73216131	0.92[EUR][1000 genomes]
rs73218207	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73218210	0.92[EUR][1000 genomes]
rs73218221	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957243	0.88[AFR][1000 genomes]
rs7959194	0.95[EUR][1000 genomes]
rs7973360	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121562400-121570600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:121562800-121569200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:121562800-121570400	Weak transcription	Ovary	ovary
4	chr12:121563000-121569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:121564000-121568600	Enhancers	Liver	Liver
6	chr12:121564200-121570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:121565200-121569600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:121565400-121568400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:121565800-121568400	Enhancers	Fetal Thymus	thymus
10	chr12:121565800-121570600	Enhancers	Placenta	Placenta
11	chr12:121566600-121570200	Weak transcription	Small Intestine	intestine
12	chr12:121566800-121568600	Enhancers	Colonic Mucosa	Colon
13	chr12:121566800-121570400	Weak transcription	Gastric	stomach
14	chr12:121567000-121570200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:121567200-121569800	Weak transcription	NHEK	skin
16	chr12:121567200-121570000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:121567200-121570400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:121567200-121570400	Weak transcription	Fetal Lung	lung
19	chr12:121567200-121570400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:121567200-121570400	Weak transcription	HMEC	breast
21	chr12:121567400-121570400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:121567400-121570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:121567400-121570400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:121567600-121568400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr12:121567600-121568400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:121567600-121568400	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr12:121567600-121568400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:121567600-121569000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:121567600-121569000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:121567600-121569400	Weak transcription	K562	blood
31	chr12:121567600-121569600	Weak transcription	HUVEC	blood vessel
32	chr12:121567600-121569800	Enhancers	Brain Angular Gyrus	brain
33	chr12:121567600-121569800	Weak transcription	Fetal Intestine Small	intestine
34	chr12:121567600-121570000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:121567600-121570000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:121567600-121570000	Enhancers	Brain Substantia Nigra	brain
37	chr12:121567600-121570200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:121567600-121570200	Weak transcription	Fetal Heart	heart
39	chr12:121567600-121570200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:121567600-121570200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:121567600-121570400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:121567600-121570400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr12:121567600-121570400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:121567600-121570400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr12:121567600-121570400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr12:121567600-121570400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:121567600-121570400	Weak transcription	Psoas Muscle	Psoas
48	chr12:121567600-121570400	Weak transcription	Right Atrium	heart
49	chr12:121567600-121570400	Weak transcription	Right Ventricle	heart
50	chr12:121567600-121570400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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