Variant report

Variant	rs10229453
Chromosome Location	chr7:100658717-100658718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100462781..100465423-chr7:100657982..100660007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087077	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10447810	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808115	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953314	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11766024	0.84[ASN][1000 genomes]
rs11766048	0.89[ASN][1000 genomes]
rs11766125	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11771829	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772812	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11772963	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532750	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12538004	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12540832	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13242391	0.81[ASN][1000 genomes]
rs34547547	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3891963	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3924886	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4370452	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4605982	0.83[ASN][1000 genomes]
rs55869514	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67047657	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6973913	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs7457468	0.83[ASN][1000 genomes]
rs7785171	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1836983	chr7:100630638-100669857	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	esv1849981	chr7:100633668-100686761	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv1828583	chr7:100652181-100676353	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv1823966	chr7:100652181-100693849	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10229453	PMS2L1	cis	cerebellum	SCAN
rs10229453	BRI3	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100635400-100660000	Weak transcription	Gastric	stomach
2	chr7:100635800-100660000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:100635800-100660200	Weak transcription	Right Atrium	heart
4	chr7:100647800-100659000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr7:100647800-100660200	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr7:100648800-100659000	Weak transcription	Spleen	Spleen
7	chr7:100651000-100658800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:100651600-100660000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:100652000-100659200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:100652200-100658800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:100652600-100660000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:100653400-100659800	Weak transcription	NHLF	lung
13	chr7:100653600-100659000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr7:100653600-100659200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:100653800-100660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:100653800-100660000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:100654200-100658800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:100654200-100659800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:100654400-100658800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:100654400-100659200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:100655200-100658800	Weak transcription	GM12878-XiMat	blood
22	chr7:100655200-100659800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:100655400-100659600	Strong transcription	Colonic Mucosa	Colon
24	chr7:100655600-100659000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:100655800-100659200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr7:100655800-100659600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:100656000-100659200	Weak transcription	Stomach Mucosa	stomach
28	chr7:100656200-100659200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:100656600-100658800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:100656600-100660000	Weak transcription	Thymus	Thymus
31	chr7:100657000-100660000	Weak transcription	HSMMtube	muscle
32	chr7:100657200-100658800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:100657200-100659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:100657400-100658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:100657400-100659200	Weak transcription	Fetal Intestine Large	intestine
36	chr7:100657400-100660000	Weak transcription	Fetal Brain Male	brain
37	chr7:100657600-100660000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr7:100657600-100660000	Weak transcription	Fetal Intestine Small	intestine
39	chr7:100657600-100660000	Weak transcription	Ovary	ovary
40	chr7:100657600-100660000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:100658400-100659800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:100658600-100659400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:100658600-100659600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:100658600-100659800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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