Variant report

Variant	rs12299386
Chromosome Location	chr12:50060528-50060529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50053639..50056299-chr12:50060265..50061800,2	K562	blood:
2	chr12:50059879..50062225-chr12:50063774..50067547,4	K562	blood:
3	chr12:50058737..50060744-chr12:50060890..50062454,2	K562	blood:
4	chr12:50059406..50061559-chr12:50099659..50102514,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction
ENSG00000161791	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10047567	1.00[AFR][1000 genomes]
rs10467104	1.00[AFR][1000 genomes]
rs11169030	1.00[AFR][1000 genomes]
rs11169036	1.00[AFR][1000 genomes]
rs11169072	1.00[AFR][1000 genomes]
rs11169077	1.00[AFR][1000 genomes]
rs11169096	1.00[AFR][1000 genomes]
rs11169119	1.00[AFR][1000 genomes]
rs12301239	1.00[AFR][1000 genomes]
rs12310439	1.00[AFR][1000 genomes]
rs12313145	1.00[AFR][1000 genomes]
rs12322413	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50042400-50067000	Weak transcription	Fetal Brain Male	brain
2	chr12:50052200-50066200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:50052400-50064800	Weak transcription	Fetal Kidney	kidney
4	chr12:50052600-50067000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:50052600-50067400	Weak transcription	Fetal Brain Female	brain
6	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
7	chr12:50054600-50061000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr12:50055400-50060800	Genic enhancers	Fetal Stomach	stomach
9	chr12:50055400-50061400	Enhancers	Brain Substantia Nigra	brain
10	chr12:50055600-50062400	Enhancers	Psoas Muscle	Psoas
11	chr12:50057400-50063800	Weak transcription	Ovary	ovary
12	chr12:50057400-50066200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:50057600-50060800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:50057600-50063200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:50057600-50064400	Weak transcription	Gastric	stomach
16	chr12:50057600-50064400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:50057600-50064400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr12:50057600-50064800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:50057600-50065000	Weak transcription	Pancreas	Pancrea
20	chr12:50057600-50065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:50057600-50066000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:50057600-50066200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:50057600-50066400	Weak transcription	Aorta	Aorta
24	chr12:50057600-50066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:50057600-50067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:50057600-50067000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:50057600-50067200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:50057800-50063800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr12:50057800-50066200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:50058000-50062600	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:50058200-50062000	Genic enhancers	Primary B cells from cord blood	blood
32	chr12:50058400-50061000	Genic enhancers	Thymus	Thymus
33	chr12:50058400-50062000	Genic enhancers	Primary B cells from peripheral blood	blood
34	chr12:50058400-50064400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:50058400-50066000	Weak transcription	Esophagus	oesophagus
36	chr12:50058400-50067200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:50058600-50061200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:50058800-50060800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:50058800-50061200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:50058800-50061400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:50058800-50061800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:50058800-50063800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:50058800-50063800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:50058800-50064600	Weak transcription	K562	blood
45	chr12:50058800-50066000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:50059000-50061200	Weak transcription	NHDF-Ad	bronchial
47	chr12:50059000-50061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:50059000-50063000	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:50059000-50063200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:50059000-50063600	Weak transcription	Dnd41	blood

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