Variant report

Variant	rs2708611
Chromosome Location	chr7:112101595-112101596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112088811..112094041-chr7:112100770..112110657,18	MCF-7	breast:
2	chr7:112100687..112102233-chr7:112105743..112108488,2	MCF-7	breast:
3	chr7:112097815..112102397-chr7:112106064..112108560,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1468458	1.00[YRI][hapmap]
rs2074796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2253962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2529588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708609	0.86[ASN][1000 genomes]
rs2708610	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3095025	0.91[ASN][1000 genomes]
rs3109112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3128386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3128388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3183621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3807213	0.91[YRI][hapmap]
rs4386904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967593	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs7467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1801262	chr7:112071795-112104179	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2708611	LSMEM1	cis	Thyroid	GTEx
rs2708611	IFRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112102400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:112092600-112109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:112093000-112109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:112094000-112102200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:112094600-112102200	Weak transcription	Fetal Brain Male	brain
10	chr7:112094600-112105200	Strong transcription	K562	blood
11	chr7:112094600-112109800	Weak transcription	Small Intestine	intestine
12	chr7:112094600-112114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:112094600-112117000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:112094800-112101600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:112095000-112114200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:112095200-112109800	Weak transcription	Right Ventricle	heart
17	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:112095400-112105200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr7:112095400-112108000	Strong transcription	Fetal Intestine Large	intestine
20	chr7:112095400-112117200	Strong transcription	Dnd41	blood
21	chr7:112095600-112101600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:112095600-112102000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:112095600-112102000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:112095600-112102000	Strong transcription	NHDF-Ad	bronchial
25	chr7:112095600-112102200	Strong transcription	HMEC	breast
26	chr7:112095600-112116400	Strong transcription	NH-A	brain
27	chr7:112095600-112116600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:112095600-112117200	Strong transcription	HSMM	muscle
29	chr7:112095600-112117400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:112095600-112117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:112095600-112117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:112095800-112101600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:112095800-112101600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr7:112095800-112102000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:112095800-112102000	Strong transcription	Adipose Nuclei	Adipose
37	chr7:112095800-112102000	Strong transcription	Colon Smooth Muscle	Colon
38	chr7:112095800-112102000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:112095800-112102000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:112095800-112102400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:112095800-112103400	Strong transcription	Fetal Lung	lung
42	chr7:112095800-112103600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr7:112095800-112104800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr7:112095800-112105200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:112095800-112105400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr7:112095800-112114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:112095800-112117000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr7:112095800-112117000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:112095800-112117400	Strong transcription	Fetal Thymus	thymus
50	chr7:112095800-112118000	Strong transcription	Placenta	Placenta

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