Variant report

Variant	rs28508138
Chromosome Location	chr12:122029219-122029220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121993318..121995830-chr12:122027448..122029552,2	K562	blood:
2	chr12:122014726..122017579-chr12:122028385..122031579,3	MCF-7	breast:
3	chr12:122027393..122030554-chr12:122096277..122098532,3	K562	blood:

Variant related genes	Relation type
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs28378998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397246	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28489288	0.84[AMR][1000 genomes]
rs28517331	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28546504	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28552516	0.82[AMR][1000 genomes]
rs28594507	0.84[AMR][1000 genomes]
rs73227906	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73227912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122020600-122030200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:122020800-122040400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:122021200-122036000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:122021600-122033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:122028200-122031800	Enhancers	Placenta	Placenta
6	chr12:122028200-122038800	Weak transcription	Pancreas	Pancrea
7	chr12:122028600-122048000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:122028600-122048400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:122028800-122029400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:122028800-122029400	Enhancers	Fetal Stomach	stomach
11	chr12:122028800-122029400	Weak transcription	Psoas Muscle	Psoas
12	chr12:122028800-122029800	Enhancers	Fetal Muscle Trunk	muscle
13	chr12:122028800-122030600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:122028800-122030600	Enhancers	Fetal Thymus	thymus
15	chr12:122028800-122032000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:122028800-122032400	Weak transcription	Brain Anterior Caudate	brain
17	chr12:122028800-122033600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:122028800-122036000	Weak transcription	Fetal Intestine Small	intestine
19	chr12:122028800-122048400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:122028800-122049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
22	chr12:122029000-122029400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:122029000-122030600	Enhancers	Primary B cells from peripheral blood	blood
24	chr12:122029000-122033400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:122029200-122029400	Enhancers	Dnd41	blood
26	chr12:122029200-122029600	Enhancers	Thymus	Thymus
27	chr12:122029200-122029800	Enhancers	Primary B cells from cord blood	blood
28	chr12:122029200-122029800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:122029200-122029800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:122029200-122030200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:122029200-122030200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:122029200-122030200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:122029200-122030200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:122029200-122030200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:122029200-122030200	Weak transcription	HepG2	liver
36	chr12:122029200-122030200	Weak transcription	NHDF-Ad	bronchial
37	chr12:122029200-122030400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:122029200-122030400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:122029200-122030400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:122029200-122030400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr12:122029200-122030400	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:122029200-122030600	Enhancers	Primary T cells from cord blood	blood
43	chr12:122029200-122030600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:122029200-122030600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr12:122029200-122030600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr12:122029200-122030600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr12:122029200-122030600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr12:122029200-122030600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:122029200-122030600	Enhancers	GM12878-XiMat	blood
50	chr12:122029200-122030800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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