Variant report

Variant	rs28560293
Chromosome Location	chr7:66239344-66239345
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	chr7:66233619..66236445-chr7:66238794..66241787,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10226191	0.81[AFR][1000 genomes]
rs10231411	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10234322	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10234747	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10235638	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10241395	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10241528	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10242870	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10243608	0.80[EUR][1000 genomes]
rs10244459	0.80[EUR][1000 genomes]
rs10247324	0.84[EUR][1000 genomes]
rs10250124	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10252133	0.83[ASN][1000 genomes]
rs10257393	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10258628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10262184	0.83[ASN][1000 genomes]
rs10263993	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10264223	0.82[AFR][1000 genomes]
rs10265069	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10267253	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10267834	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10273320	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10275343	0.82[AFR][1000 genomes]
rs10278343	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10281090	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10282310	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10282522	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479728	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1060527	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1064795	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12234826	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12334214	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13438432	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013707	0.81[EUR][1000 genomes]
rs28368585	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28379824	0.86[EUR][1000 genomes]
rs28460006	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28533332	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28547918	0.83[EUR][1000 genomes]
rs28634091	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs28663128	0.83[EUR][1000 genomes]
rs28729561	0.82[AFR][1000 genomes]
rs3778907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778908	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3800814	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3823607	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3823609	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3962133	0.80[EUR][1000 genomes]
rs4718417	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56743740	0.82[AFR][1000 genomes]
rs57774708	0.81[AFR][1000 genomes]
rs60026498	0.81[AFR][1000 genomes]
rs60972148	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67408913	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6974601	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73133851	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73139941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73139976	0.80[EUR][1000 genomes]
rs73141980	0.81[AFR][1000 genomes]
rs73143998	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7455757	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7777631	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7796977	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28560293	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs28560293	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
4	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
5	chr7:66214400-66239400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:66216800-66239400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:66221800-66240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:66227000-66243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
11	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:66233000-66241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:66233200-66239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:66234000-66239400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:66234200-66241800	Weak transcription	Small Intestine	intestine
17	chr7:66234600-66239400	Weak transcription	Pancreas	Pancrea
18	chr7:66234800-66243600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:66235000-66240400	Weak transcription	K562	blood
21	chr7:66235200-66239400	Weak transcription	Fetal Kidney	kidney
22	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:66235400-66239600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:66235400-66239600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:66235400-66241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
27	chr7:66235600-66239400	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:66235800-66239400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr7:66235800-66239600	Weak transcription	Colonic Mucosa	Colon
30	chr7:66236000-66239400	Weak transcription	NHLF	lung
31	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
32	chr7:66236600-66241000	Strong transcription	Fetal Intestine Small	intestine
33	chr7:66236600-66244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:66236800-66242400	Strong transcription	HSMM	muscle
35	chr7:66236800-66242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:66236800-66243400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:66236800-66243800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:66236800-66244800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:66236800-66245400	Strong transcription	GM12878-XiMat	blood
40	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr7:66236800-66276800	Strong transcription	Dnd41	blood
43	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:66237000-66239600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:66237000-66243800	Strong transcription	Fetal Thymus	thymus
47	chr7:66237000-66244800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:66237000-66245000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:66237000-66245400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:66237200-66239400	Weak transcription	H1 Cell Line	embryonic stem cell

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