Variant report

Variant	rs7978536
Chromosome Location	chr12:122189520-122189521
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
2	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
3	chr12:122147215..122155218-chr12:122185094..122190846,22	MCF-7	breast:
4	chr12:122180307..122183056-chr12:122185275..122189745,5	K562	blood:
5	chr12:122188399..122190349-chr12:122238122..122239651,2	K562	blood:

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1107243	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs28656299	0.92[EUR][1000 genomes]
rs3970421	0.97[EUR][1000 genomes]
rs55775605	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56379201	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56959328	0.92[EUR][1000 genomes]
rs57318156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57611711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58274150	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58534280	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58986108	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61230721	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6486775	0.80[EUR][1000 genomes]
rs7294817	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7310523	0.80[EUR][1000 genomes]
rs7313408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73411779	0.92[EUR][1000 genomes]
rs73411780	0.92[EUR][1000 genomes]
rs73411782	0.92[EUR][1000 genomes]
rs73411785	0.92[EUR][1000 genomes]
rs73411786	0.97[EUR][1000 genomes]
rs7957751	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7962125	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7965407	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7968717	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980551	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9737587	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9739927	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv560472	chr12:122185258-122190385	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv560489	chr12:122185616-122190385	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7978536	RHOF	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122152200-122191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:122152200-122191600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
5	chr12:122159400-122194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:122174200-122191800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:122179800-122211000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:122180200-122191400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
10	chr12:122184800-122191600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:122184800-122208000	Weak transcription	Colonic Mucosa	Colon
12	chr12:122185000-122191400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:122186200-122190000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:122186200-122190200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:122186200-122190600	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr12:122186200-122193600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:122186200-122194000	Strong transcription	Fetal Brain Female	brain
18	chr12:122186200-122197400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:122186400-122189600	Weak transcription	Liver	Liver
20	chr12:122186400-122190200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:122186400-122190400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr12:122186400-122191200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:122186400-122191200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:122186600-122190200	Strong transcription	HSMMtube	muscle
25	chr12:122186600-122191200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:122186600-122192200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:122186600-122200400	Weak transcription	Right Atrium	heart
28	chr12:122186800-122190200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:122186800-122191600	Weak transcription	Spleen	Spleen
30	chr12:122186800-122191800	Weak transcription	Left Ventricle	heart
31	chr12:122186800-122197200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:122187000-122191000	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:122187000-122192200	Weak transcription	Brain Angular Gyrus	brain
34	chr12:122187000-122192200	Weak transcription	Fetal Brain Male	brain
35	chr12:122187000-122192600	Weak transcription	NHDF-Ad	bronchial
36	chr12:122187000-122195200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:122187000-122199600	Strong transcription	Fetal Stomach	stomach
38	chr12:122187000-122207600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:122187000-122208200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:122187200-122189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:122187200-122190200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:122187200-122191600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:122187200-122191800	Weak transcription	Fetal Kidney	kidney
44	chr12:122187200-122203400	Weak transcription	Hela-S3	cervix
45	chr12:122187200-122205600	Weak transcription	Fetal Lung	lung
46	chr12:122187400-122189600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:122187400-122189800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:122187400-122189800	Weak transcription	Esophagus	oesophagus
49	chr12:122187400-122190400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:122187400-122194600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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