Variant report

Variant	rs13184538
Chromosome Location	chr5:112621408-112621409
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	chr5:112619318..112622139-chr5:112627969..112630686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10038521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10051115	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10053341	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10061462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10434754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10477490	0.86[ASN][1000 genomes]
rs1157696	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13154300	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13159509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13164135	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171482	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13174075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13174151	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13174206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13177853	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13180516	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13180522	0.86[ASN][1000 genomes]
rs13181534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13181732	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13181944	0.90[ASN][1000 genomes]
rs13183383	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13187823	0.90[ASN][1000 genomes]
rs13189050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13189910	0.86[ASN][1000 genomes]
rs1602862	0.81[ASN][1000 genomes]
rs17325307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17325503	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17325825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327964	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17388260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17389165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1838206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922678	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1922679	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2248930	0.86[CHB][hapmap]
rs34316732	0.86[ASN][1000 genomes]
rs34558181	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34682492	0.86[ASN][1000 genomes]
rs348928	0.86[CHB][hapmap]
rs348929	0.86[CHB][hapmap]
rs348930	0.86[CHB][hapmap]
rs348931	0.86[CHB][hapmap]
rs348932	0.86[CHB][hapmap]
rs348961	0.86[CHB][hapmap]
rs348962	0.86[CHB][hapmap]
rs348963	0.86[CHB][hapmap]
rs34951736	0.90[ASN][1000 genomes]
rs35359071	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35886114	0.86[ASN][1000 genomes]
rs367943	0.86[CHB][hapmap]
rs4438866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs444322	0.86[CHB][hapmap]
rs455435	0.86[CHB][hapmap]
rs460079	0.86[CHB][hapmap]
rs463167	0.86[CHB][hapmap]
rs463249	0.86[CHB][hapmap]
rs58268366	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644154	0.86[CHB][hapmap]
rs6594698	0.93[EUR][1000 genomes]
rs6594706	0.86[ASN][1000 genomes]
rs6594713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6594714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6594715	0.86[ASN][1000 genomes]
rs6594716	0.86[ASN][1000 genomes]
rs66572866	0.90[ASN][1000 genomes]
rs67320720	0.90[ASN][1000 genomes]
rs67693032	0.90[ASN][1000 genomes]
rs6870401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6871934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6872490	0.86[ASN][1000 genomes]
rs6874175	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6880562	0.90[ASN][1000 genomes]
rs6883102	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6887482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6887914	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6889489	0.86[ASN][1000 genomes]
rs6890874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6896843	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs71577442	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71577447	0.90[ASN][1000 genomes]
rs71577448	0.90[ASN][1000 genomes]
rs72792189	0.81[ASN][1000 genomes]
rs7701895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7709646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7714221	0.86[ASN][1000 genomes]
rs7714760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7717630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7718616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7720414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725712	0.86[ASN][1000 genomes]
rs7727056	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7727501	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7731231	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7734576	0.86[ASN][1000 genomes]
rs7737512	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
2	chr5:112608000-112628200	Weak transcription	HMEC	breast
3	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:112610800-112623200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112612000-112623800	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:112612000-112625200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112612200-112625200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112614200-112625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:112615000-112625200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112616800-112623400	Weak transcription	NHEK	skin
12	chr5:112616800-112623800	Weak transcription	Esophagus	oesophagus
13	chr5:112617000-112622000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:112617400-112621600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:112617800-112625400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:112617800-112628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:112618200-112623600	Weak transcription	Gastric	stomach
18	chr5:112618400-112628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:112618400-112628200	Weak transcription	Fetal Kidney	kidney
20	chr5:112618400-112628200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:112618400-112628400	Weak transcription	Fetal Stomach	stomach
22	chr5:112618600-112625600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:112618800-112622000	Weak transcription	Brain Angular Gyrus	brain
24	chr5:112619000-112626800	Weak transcription	Liver	Liver
25	chr5:112619000-112628600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:112619000-112628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:112619200-112625600	Weak transcription	Fetal Lung	lung
28	chr5:112619400-112621800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:112619400-112624000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:112619400-112625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:112619600-112625200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:112619800-112621600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:112620000-112621600	Weak transcription	Fetal Heart	heart
34	chr5:112620000-112628200	Weak transcription	Brain Anterior Caudate	brain
35	chr5:112620000-112628200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:112620400-112621600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr5:112620400-112625200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:112621000-112622400	Enhancers	Ovary	ovary
39	chr5:112621200-112621600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr5:112621200-112621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:112621200-112621600	Enhancers	Brain Substantia Nigra	brain
42	chr5:112621200-112622000	Enhancers	Right Ventricle	heart
43	chr5:112621200-112622200	Enhancers	Left Ventricle	heart
44	chr5:112621200-112622200	Enhancers	Psoas Muscle	Psoas
45	chr5:112621200-112622400	Enhancers	Adipose Nuclei	Adipose
46	chr5:112621200-112622400	Enhancers	Right Atrium	heart
47	chr5:112621200-112622800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:112621400-112621800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links