Variant report

Variant	rs11204906
Chromosome Location	chr1:151841165-151841166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151822231..151823939-chr1:151841022..151843082,2	MCF-7	breast:
2	chr1:151832485..151835043-chr1:151841039..151843402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196407	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10494270	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11582739	0.83[AMR][1000 genomes]
rs12083193	0.81[AMR][1000 genomes]
rs12095483	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12566232	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833668	0.85[AMR][1000 genomes]
rs16833669	0.85[AMR][1000 genomes]
rs16833670	0.85[AMR][1000 genomes]
rs16833743	0.81[AMR][1000 genomes]
rs1844543	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2337685	0.85[AMR][1000 genomes]
rs2337686	0.85[AMR][1000 genomes]
rs2338206	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28415528	0.82[EUR][1000 genomes]
rs3791153	0.81[AMR][1000 genomes]
rs56000812	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56028913	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56078223	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56170235	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56313205	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57674198	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57785325	0.85[AMR][1000 genomes]
rs58087484	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61817695	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61817697	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61817719	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817720	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61817722	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817724	0.85[AMR][1000 genomes]
rs61817725	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6587632	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587633	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6587634	0.85[AMR][1000 genomes]
rs6659662	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6662602	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6663064	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671719	0.85[AFR][1000 genomes]
rs6672064	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6675930	0.85[AMR][1000 genomes]
rs6678672	0.82[AMR][1000 genomes]
rs6682605	0.82[AMR][1000 genomes]
rs6684114	0.85[AMR][1000 genomes]
rs6684312	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6686874	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6690449	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693388	0.85[AMR][1000 genomes]
rs6693396	0.85[AMR][1000 genomes]
rs6693901	0.85[AMR][1000 genomes]
rs6695324	0.85[AMR][1000 genomes]
rs6701374	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6703448	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72694840	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7535002	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7538652	0.84[AMR][1000 genomes]
rs7554859	0.82[AMR][1000 genomes]
rs9943221	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9943251	0.87[AMR][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	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11204906	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs11204906	THEM4	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
2	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:151826400-151846200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151829000-151845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:151831000-151881400	Weak transcription	Ovary	ovary
6	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151832800-151846000	Weak transcription	Spleen	Spleen
8	chr1:151834000-151849600	Weak transcription	Esophagus	oesophagus
9	chr1:151835600-151847600	Weak transcription	HSMMtube	muscle
10	chr1:151837200-151845600	Weak transcription	Lung	lung
11	chr1:151837400-151846000	Weak transcription	Left Ventricle	heart
12	chr1:151837600-151845400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:151837600-151845400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:151837600-151845400	Weak transcription	Right Ventricle	heart
15	chr1:151837800-151846200	Weak transcription	Fetal Thymus	thymus
16	chr1:151838800-151841600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:151839600-151845800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:151839800-151841400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:151839800-151841400	Enhancers	Hela-S3	cervix
20	chr1:151840000-151841200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:151840000-151841200	Enhancers	NHEK	skin
22	chr1:151840000-151841400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:151840000-151841600	Enhancers	HUVEC	blood vessel
24	chr1:151840200-151841200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:151840200-151841600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:151840200-151841800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:151840200-151846000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:151840400-151841200	Enhancers	HMEC	breast
29	chr1:151840400-151841200	Enhancers	NHLF	lung
30	chr1:151840400-151841400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151840400-151841400	Enhancers	Osteobl	bone
32	chr1:151840400-151845400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:151840400-151846000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:151840600-151841200	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr1:151840600-151846000	Weak transcription	Adipose Nuclei	Adipose
36	chr1:151840600-151864600	Weak transcription	NH-A	brain
37	chr1:151840800-151841200	Active TSS	Brain Hippocampus Middle	brain
38	chr1:151840800-151841200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:151840800-151843800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:151840800-151845400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:151840800-151845400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:151840800-151846000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:151840800-151847600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:151840800-151857800	Weak transcription	K562	blood
45	chr1:151841000-151841200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:151841000-151841200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:151841000-151841200	Enhancers	Brain Anterior Caudate	brain
48	chr1:151841000-151841200	Enhancers	Fetal Stomach	stomach
49	chr1:151841000-151843600	Weak transcription	Placenta	Placenta
50	chr1:151841000-151845800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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