Variant report

Variant	rs28569300
Chromosome Location	chr5:40691665-40691666
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	chr5:40678816..40680849-chr5:40690790..40692846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10056345	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060234	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10064175	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13355305	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154268	0.85[ASN][1000 genomes]
rs154275	0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs171605	0.85[ASN][1000 genomes]
rs193864	0.84[ASN][1000 genomes]
rs2161521	0.85[ASN][1000 genomes]
rs249413	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs249414	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249416	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249420	0.83[ASN][1000 genomes]
rs249422	0.85[ASN][1000 genomes]
rs249423	0.85[ASN][1000 genomes]
rs249425	0.85[ASN][1000 genomes]
rs249428	0.85[ASN][1000 genomes]
rs249429	0.85[ASN][1000 genomes]
rs257009	0.84[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	0.85[ASN][1000 genomes]
rs29743	0.85[ASN][1000 genomes]
rs29744	0.85[ASN][1000 genomes]
rs4277957	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4285273	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4315964	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4315965	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432071	0.85[ASN][1000 genomes]
rs434778	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4383756	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs447810	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453037	0.85[ASN][1000 genomes]
rs4573034	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs461404	0.85[ASN][1000 genomes]
rs466108	0.85[ASN][1000 genomes]
rs466962	0.84[ASN][1000 genomes]
rs4957344	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59069340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59920139	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451535	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451537	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6871999	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896993	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7708680	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7726237	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7733162	0.80[AMR][1000 genomes]
rs7737044	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs837101	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28569300	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs28569300	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40683000-40692000	Weak transcription	Gastric	stomach
2	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
3	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
4	chr5:40685400-40691800	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:40685400-40692000	Weak transcription	Aorta	Aorta
6	chr5:40686800-40692000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:40687800-40691800	Weak transcription	Small Intestine	intestine
8	chr5:40688200-40693800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:40688400-40696400	Weak transcription	Liver	Liver
10	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
11	chr5:40688800-40691800	Weak transcription	Fetal Intestine Large	intestine
12	chr5:40688800-40691800	Weak transcription	Thymus	Thymus
13	chr5:40688800-40692000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:40688800-40692800	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr5:40688800-40694600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:40688800-40696800	Weak transcription	Fetal Lung	lung
17	chr5:40688800-40697000	Strong transcription	Fetal Thymus	thymus
18	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:40689000-40691800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:40689000-40692000	Weak transcription	Primary B cells from cord blood	blood
21	chr5:40689600-40693000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:40689600-40694400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr5:40690000-40692800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:40690000-40695800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:40690200-40692800	Strong transcription	Fetal Intestine Small	intestine
26	chr5:40690200-40693000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr5:40690200-40693200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr5:40690200-40694200	Weak transcription	Osteobl	bone
29	chr5:40690200-40694600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr5:40690200-40695200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:40690400-40692000	Weak transcription	NH-A	brain
32	chr5:40690400-40693000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:40690400-40695200	Strong transcription	HSMM	muscle
34	chr5:40690400-40697200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:40690600-40691800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:40690600-40691800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:40690600-40691800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:40690600-40691800	Weak transcription	HMEC	breast
39	chr5:40690600-40691800	Weak transcription	HSMMtube	muscle
40	chr5:40690600-40692000	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:40690600-40692000	Weak transcription	NHLF	lung
42	chr5:40690600-40692600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:40690600-40693000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:40690600-40695400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:40690800-40691800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:40690800-40691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:40690800-40692000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:40690800-40692200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:40690800-40692600	Genic enhancers	Dnd41	blood
50	chr5:40690800-40692800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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