Variant report

Variant	rs28546848
Chromosome Location	chr12:56538161-56538162
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56531111..56535117-chr12:56537564..56540516,4	MCF-7	breast:
2	chr12:56536501..56538802-chr12:56552198..56554579,2	MCF-7	breast:
3	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:
4	chr12:56518356..56534331-chr12:56534720..56548698,49	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYL6B-1	chr12:56537607-56538175	NONHSAT028775

Variant related genes	Relation type
ENSG00000229117	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10129008	0.82[AFR][1000 genomes]
rs11171746	0.93[AFR][1000 genomes]
rs11171754	0.93[AFR][1000 genomes]
rs11171755	0.93[AFR][1000 genomes]
rs11171760	1.00[EUR][1000 genomes]
rs11504023	0.89[AFR][1000 genomes]
rs11837267	1.00[EUR][1000 genomes]
rs12296387	0.90[AFR][1000 genomes]
rs12298136	0.93[AFR][1000 genomes]
rs12298822	1.00[EUR][1000 genomes]
rs12306670	1.00[EUR][1000 genomes]
rs12308473	1.00[EUR][1000 genomes]
rs12309692	0.93[AFR][1000 genomes]
rs17852368	1.00[EUR][1000 genomes]
rs2450101	1.00[EUR][1000 genomes]
rs2629453	1.00[EUR][1000 genomes]
rs28676339	0.93[AFR][1000 genomes]
rs56163805	1.00[EUR][1000 genomes]
rs59499104	1.00[EUR][1000 genomes]
rs73340385	1.00[EUR][1000 genomes]
rs73340390	1.00[EUR][1000 genomes]
rs7397951	1.00[EUR][1000 genomes]
rs772925	1.00[EUR][1000 genomes]
rs772926	1.00[EUR][1000 genomes]
rs773654	1.00[EUR][1000 genomes]
rs773663	1.00[EUR][1000 genomes]
rs7967464	1.00[EUR][1000 genomes]
rs7975486	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56523800-56539400	Strong transcription	NHEK	skin
2	chr12:56524200-56539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:56524200-56539200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:56524200-56539400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:56524200-56539400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:56524200-56539400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:56524200-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:56524200-56539400	Strong transcription	NH-A	brain
9	chr12:56524400-56539000	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr12:56524400-56539000	Strong transcription	Rectal Smooth Muscle	rectum
11	chr12:56524400-56539000	Strong transcription	HSMMtube	muscle
12	chr12:56524400-56539200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:56524400-56539200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:56524400-56539200	Strong transcription	Fetal Stomach	stomach
15	chr12:56524400-56539400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:56524400-56539400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:56524400-56539400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:56524400-56539400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:56524400-56539400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:56524400-56539400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:56524400-56539400	Strong transcription	Liver	Liver
22	chr12:56524400-56539600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:56524600-56538600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:56524600-56538800	Strong transcription	Fetal Brain Female	brain
25	chr12:56524600-56539000	Strong transcription	Colon Smooth Muscle	Colon
26	chr12:56524600-56539200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:56524600-56539400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:56524600-56539400	Strong transcription	HSMM	muscle
29	chr12:56524600-56539400	Strong transcription	NHDF-Ad	bronchial
30	chr12:56525000-56539400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:56525000-56539400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:56525000-56539400	Strong transcription	Fetal Lung	lung
33	chr12:56525000-56539400	Strong transcription	K562	blood
34	chr12:56525400-56539200	Strong transcription	Thymus	Thymus
35	chr12:56525800-56539200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:56526600-56539400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr12:56527200-56540000	Weak transcription	Fetal Heart	heart
38	chr12:56528200-56545200	Weak transcription	Stomach Mucosa	stomach
39	chr12:56529400-56539000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:56529800-56539400	Strong transcription	Brain Germinal Matrix	brain
41	chr12:56530000-56539200	Strong transcription	Osteobl	bone
42	chr12:56530000-56539400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:56530200-56539000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr12:56530200-56539000	Strong transcription	Aorta	Aorta
45	chr12:56530200-56539400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:56530400-56538800	Strong transcription	Pancreas	Pancrea
47	chr12:56530400-56539000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:56530400-56539000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:56530400-56539000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:56530400-56539000	Strong transcription	Gastric	stomach

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