Variant report

Variant	rs9282
Chromosome Location	chr12:122219910-122219911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122217817..122222625-chr12:122235790..122242692,8	K562	blood:
2	chr12:122219403..122222568-chr12:122228956..122233435,5	K562	blood:
3	chr12:122218052..122221666-chr12:122223927..122226116,4	MCF-7	breast:
4	chr12:122139575..122141363-chr12:122218691..122220563,2	MCF-7	breast:
5	chr12:122219448..122221422-chr12:122224935..122227842,2	MCF-7	breast:
6	chr12:122219428..122221615-chr12:122247331..122249175,2	K562	blood:
7	chr12:122213667..122215925-chr12:122218453..122221543,3	MCF-7	breast:
8	chr12:122218382..122220105-chr12:122236095..122239038,2	K562	blood:
9	chr12:122217066..122219995-chr12:122220346..122223627,4	MCF-7	breast:
10	chr12:122216581..122218765-chr12:122219403..122221969,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETD1B-4	chr12:122218847-122220907	NONHSAT031439

No data

Variant related genes	Relation type
ENSG00000212694	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10082850	0.90[EUR][1000 genomes]
rs11834522	0.94[EUR][1000 genomes]
rs11837955	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12299238	0.90[EUR][1000 genomes]
rs12303659	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12310051	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12312375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12314801	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs12318048	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832268	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12832320	0.97[EUR][1000 genomes]
rs28493021	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34226605	0.97[EUR][1000 genomes]
rs34415086	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741588	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136373	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7300684	0.97[EUR][1000 genomes]
rs7308123	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs7308348	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73413728	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73413732	0.90[EUR][1000 genomes]
rs9165	0.87[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9282	RHOF	cis	parietal	SCAN
rs9282	RHOF	cis	Liver	GTEx
rs9282	SBNO1	cis	parietal	SCAN
rs9282	LRRC43	cis	multi-tissue	Pritchard
rs9282	RHOF	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
2	chr12:122206400-122228200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:122206600-122220000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:122206600-122226400	Weak transcription	Aorta	Aorta
6	chr12:122211600-122225000	Weak transcription	Psoas Muscle	Psoas
7	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:122213400-122221200	Genic enhancers	Fetal Thymus	thymus
10	chr12:122214200-122228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:122214400-122220400	Weak transcription	Right Atrium	heart
12	chr12:122214600-122220200	Weak transcription	Stomach Mucosa	stomach
13	chr12:122214600-122224200	Weak transcription	Pancreas	Pancrea
14	chr12:122214600-122224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:122215400-122223000	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr12:122217200-122222400	Weak transcription	Liver	Liver
17	chr12:122217600-122220000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:122217800-122230400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:122218600-122220000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr12:122218600-122220600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:122218800-122220000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:122218800-122220000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:122218800-122220600	Enhancers	Esophagus	oesophagus
24	chr12:122218800-122220600	Genic enhancers	Spleen	Spleen
25	chr12:122218800-122220800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:122218800-122221200	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:122219000-122220000	Genic enhancers	Primary T cells from cord blood	blood
28	chr12:122219000-122220000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:122219000-122220600	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr12:122219000-122220800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:122219000-122220800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr12:122219000-122220800	Enhancers	NH-A	brain
33	chr12:122219000-122221000	Enhancers	Fetal Muscle Trunk	muscle
34	chr12:122219000-122225000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:122219000-122227400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:122219000-122229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:122219200-122220200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:122219200-122220400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:122219200-122220600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:122219200-122220600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:122219200-122220800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:122219200-122220800	Enhancers	NHEK	skin
43	chr12:122219200-122221200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:122219200-122222800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:122219200-122224200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:122219200-122224200	Weak transcription	Gastric	stomach
47	chr12:122219200-122224400	Weak transcription	Dnd41	blood
48	chr12:122219200-122230600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:122219200-122230600	Weak transcription	Fetal Brain Female	brain
50	chr12:122219400-122220000	Enhancers	Cortex derived primary cultured neurospheres	brain

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