Variant report

Variant	rs1052202
Chromosome Location	chr12:122216036-122216037
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122214229..122218603-chr12:122325636..122328202,4	MCF-7	breast:
2	chr12:122215351..122218115-chr12:122220558..122222536,3	K562	blood:
3	chr12:122148985..122154094-chr12:122210649..122217008,11	MCF-7	breast:
4	chr12:122213395..122216201-chr12:122325531..122328146,2	MCF-7	breast:
5	chr12:121935059..121936948-chr12:122215760..122217685,2	MCF-7	breast:
6	chr12:122214138..122216054-chr12:122231373..122233377,2	K562	blood:
7	chr12:122214559..122216075-chr12:122238255..122240656,2	K562	blood:
8	chr12:122214406..122216955-chr12:122229851..122233377,3	K562	blood:
9	chr12:122212415..122216174-chr12:122326415..122328726,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SETD1B-4	chr12:122215983-122216262	NONHSAT031440

No data

Variant related genes	Relation type
ENSG00000256950	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1064169	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11043192	0.89[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs11043193	0.88[EUR][1000 genomes]
rs11043194	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs11043195	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs11043196	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs15797	0.90[JPT][hapmap]
rs3741590	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55695154	0.86[EUR][1000 genomes]
rs56012262	0.86[EUR][1000 genomes]
rs73413708	0.86[EUR][1000 genomes]
rs73413711	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73413713	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73413716	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73413717	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73413720	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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	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
4	esv1808272	chr12:122208492-122216042	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1052202	RHOF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr12:122190400-122217000	Weak transcription	Esophagus	oesophagus
3	chr12:122206000-122216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:122206400-122228200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
6	chr12:122206600-122216800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:122206600-122216800	Weak transcription	Fetal Brain Female	brain
8	chr12:122206600-122219400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:122206600-122219400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:122206600-122219400	Weak transcription	Osteobl	bone
11	chr12:122206600-122219600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:122206600-122220000	Weak transcription	Brain Anterior Caudate	brain
13	chr12:122206600-122226400	Weak transcription	Aorta	Aorta
14	chr12:122206800-122216400	Weak transcription	Brain Germinal Matrix	brain
15	chr12:122208400-122219600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:122211200-122217000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:122211400-122218200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:122211400-122219400	Weak transcription	K562	blood
19	chr12:122211600-122219200	Strong transcription	Fetal Stomach	stomach
20	chr12:122211600-122219400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:122211600-122225000	Weak transcription	Psoas Muscle	Psoas
22	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:122211800-122218600	Weak transcription	NHEK	skin
24	chr12:122211800-122219000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:122211800-122219000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:122211800-122219000	Weak transcription	NH-A	brain
27	chr12:122211800-122219200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:122211800-122219400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:122211800-122219400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:122211800-122219400	Weak transcription	HSMM	muscle
31	chr12:122211800-122219800	Weak transcription	Fetal Lung	lung
32	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
33	chr12:122212800-122217800	Genic enhancers	A549	lung
34	chr12:122212800-122219400	Weak transcription	HSMMtube	muscle
35	chr12:122213400-122221200	Genic enhancers	Fetal Thymus	thymus
36	chr12:122213600-122216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:122214000-122216200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:122214000-122216400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:122214000-122216400	Weak transcription	NHLF	lung
40	chr12:122214000-122217000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:122214000-122218400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:122214200-122219800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:122214200-122228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:122214400-122216800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:122214400-122217200	Weak transcription	Fetal Brain Male	brain
46	chr12:122214400-122220400	Weak transcription	Right Atrium	heart
47	chr12:122214600-122216200	Weak transcription	Lung	lung
48	chr12:122214600-122216200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:122214600-122216400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:122214600-122216400	Weak transcription	Primary monocytes fromperipheralblood	blood

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