Variant report

Variant	rs28656299
Chromosome Location	chr12:122205866-122205867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122204123..122206945-chr12:122208235..122211295,4	MCF-7	breast:
2	chr12:122190799..122194662-chr12:122203499..122206586,3	MCF-7	breast:
3	chr12:122200552..122202260-chr12:122204854..122206722,2	MCF-7	breast:
4	chr12:122201883..122204367-chr12:122205822..122208200,4	K562	blood:
5	chr12:122191528..122194366-chr12:122203960..122205884,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs3970421	0.94[EUR][1000 genomes]
rs55775605	0.94[EUR][1000 genomes]
rs56379201	0.94[EUR][1000 genomes]
rs56959328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57318156	0.94[EUR][1000 genomes]
rs57611711	0.94[EUR][1000 genomes]
rs58274150	0.92[EUR][1000 genomes]
rs58534280	0.94[EUR][1000 genomes]
rs58986108	0.94[EUR][1000 genomes]
rs61230721	0.94[EUR][1000 genomes]
rs7294817	0.94[EUR][1000 genomes]
rs7313408	0.94[EUR][1000 genomes]
rs73411779	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73411780	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73411782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73411785	0.89[EUR][1000 genomes]
rs73411786	0.94[EUR][1000 genomes]
rs7957751	0.94[EUR][1000 genomes]
rs7962125	0.94[EUR][1000 genomes]
rs7965407	0.94[EUR][1000 genomes]
rs7968717	0.94[EUR][1000 genomes]
rs7978536	0.92[EUR][1000 genomes]
rs7980551	0.94[EUR][1000 genomes]
rs9737587	0.94[EUR][1000 genomes]
rs9739927	0.94[EUR][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	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
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
4	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28656299	RHOF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122179800-122211000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
3	chr12:122184800-122208000	Weak transcription	Colonic Mucosa	Colon
4	chr12:122187000-122207600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:122187000-122208200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:122187400-122213800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:122187400-122213800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:122188400-122207400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:122189200-122210800	Weak transcription	GM12878-XiMat	blood
10	chr12:122189200-122211000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:122190400-122217000	Weak transcription	Esophagus	oesophagus
12	chr12:122193000-122207600	Weak transcription	Liver	Liver
13	chr12:122193000-122211000	Weak transcription	Pancreas	Pancrea
14	chr12:122193200-122211000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:122193600-122206400	Weak transcription	Fetal Intestine Large	intestine
16	chr12:122195000-122211000	Weak transcription	Fetal Thymus	thymus
17	chr12:122195000-122211200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:122195000-122211200	Weak transcription	Thymus	Thymus
19	chr12:122195000-122212600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:122195000-122213800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:122196200-122211000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:122200600-122211000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:122200800-122213800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:122201600-122206600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:122201600-122206800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:122202000-122206200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:122202600-122206400	Enhancers	NH-A	brain
28	chr12:122203400-122206000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:122203400-122206200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr12:122203400-122206600	Enhancers	Osteobl	bone
31	chr12:122203400-122208600	Weak transcription	Fetal Kidney	kidney
32	chr12:122203400-122209800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr12:122203600-122208800	Enhancers	Fetal Brain Male	brain
34	chr12:122203800-122206600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:122203800-122206800	Strong transcription	Fetal Intestine Small	intestine
36	chr12:122203800-122211000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:122204000-122206400	Enhancers	Right Ventricle	heart
38	chr12:122204000-122206600	Enhancers	Brain Anterior Caudate	brain
39	chr12:122204000-122207400	Weak transcription	HepG2	liver
40	chr12:122204000-122207800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:122204000-122211000	Weak transcription	NHEK	skin
42	chr12:122204200-122206600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:122204200-122206800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:122204200-122206800	Genic enhancers	Fetal Stomach	stomach
45	chr12:122204200-122207200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:122204200-122207800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:122204200-122207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:122204200-122208000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:122204200-122210800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:122204200-122213400	Weak transcription	Lung	lung

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