Variant report

Variant	rs2253962
Chromosome Location	chr7:112102355-112102356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1468457	0.81[AFR][1000 genomes]
rs1468458	1.00[YRI][hapmap]
rs2074796	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2529588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708609	0.86[ASN][1000 genomes]
rs2708610	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs2708611	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]
rs3095025	0.91[ASN][1000 genomes]
rs3109112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[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];0.87[AFR][1000 genomes];0.98[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3183621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3807213	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs4386904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967593	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs7467	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2253962	C7orf53	cis	cerebellum	SCAN
rs2253962	IFRD1	Cis_1M	lymphoblastoid	RTeQTL
rs2253962	C7orf53	cis	parietal	SCAN
rs2253962	LSMEM1	cis	Thyroid	GTEx
rs2253962	TMEM168	cis	cerebellum	SCAN

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	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:112094600-112105200	Strong transcription	K562	blood
9	chr7:112094600-112109800	Weak transcription	Small Intestine	intestine
10	chr7:112094600-112114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:112094600-112117000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:112095000-112114200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:112095200-112109800	Weak transcription	Right Ventricle	heart
14	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:112095400-112105200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr7:112095400-112108000	Strong transcription	Fetal Intestine Large	intestine
17	chr7:112095400-112117200	Strong transcription	Dnd41	blood
18	chr7:112095600-112116400	Strong transcription	NH-A	brain
19	chr7:112095600-112116600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:112095600-112117200	Strong transcription	HSMM	muscle
21	chr7:112095600-112117400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:112095600-112117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:112095600-112117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr7:112095800-112102400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:112095800-112103400	Strong transcription	Fetal Lung	lung
27	chr7:112095800-112103600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:112095800-112104800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr7:112095800-112105200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:112095800-112105400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr7:112095800-112114600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:112095800-112117000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr7:112095800-112117000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr7:112095800-112117400	Strong transcription	Fetal Thymus	thymus
35	chr7:112095800-112118000	Strong transcription	Placenta	Placenta
36	chr7:112095800-112118200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr7:112095800-112118200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:112096000-112105000	Strong transcription	Primary B cells from cord blood	blood
39	chr7:112096000-112105400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:112096000-112105800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr7:112096000-112105800	Strong transcription	HepG2	liver
42	chr7:112096000-112116800	Strong transcription	HUVEC	blood vessel
43	chr7:112096200-112107000	Strong transcription	GM12878-XiMat	blood
44	chr7:112096400-112103400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:112096400-112121600	Strong transcription	Liver	Liver
46	chr7:112096400-112121800	Weak transcription	Stomach Mucosa	stomach
47	chr7:112096800-112117600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr7:112097000-112103200	Strong transcription	Fetal Kidney	kidney
49	chr7:112097400-112103000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:112097800-112111400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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