Variant report

Variant	rs28740807
Chromosome Location	chr1:75205590-75205591
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	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116791	Chromatin interaction
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11162945	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1122338	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133891	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11485264	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11485299	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034724	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043726	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359750	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1581870	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2032969	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28374065	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28445096	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28515016	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28563168	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28575168	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28719150	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28804147	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28810187	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806161	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819946	0.83[AMR][1000 genomes]
rs3819947	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650004	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650007	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4650287	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4650288	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58715708	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60292279	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681874	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745108	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535692	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540514	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs768223	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28740807	TYW3	cis	Heart Left Ventricle	GTEx
rs28740807	TYW3	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75199600-75206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:75199800-75207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
5	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
6	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
7	chr1:75201000-75206000	Strong transcription	Fetal Lung	lung
8	chr1:75201200-75206200	Strong transcription	HSMM	muscle
9	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
12	chr1:75201400-75231800	Strong transcription	Dnd41	blood
13	chr1:75201600-75206200	Strong transcription	HUVEC	blood vessel
14	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:75202200-75207400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:75202200-75207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:75202400-75205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:75202400-75205800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:75202400-75206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:75202400-75206200	Strong transcription	HSMMtube	muscle
22	chr1:75202400-75206400	Strong transcription	Brain Angular Gyrus	brain
23	chr1:75202400-75206600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:75202400-75207800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:75202400-75208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:75202400-75208000	Strong transcription	K562	blood
27	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
29	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
31	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:75202400-75213000	Strong transcription	Liver	Liver
36	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
39	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:75202600-75205800	Strong transcription	NHDF-Ad	bronchial
44	chr1:75202600-75206000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:75202600-75206400	Strong transcription	A549	lung
46	chr1:75202600-75207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:75202600-75211000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:75202600-75212400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:75202600-75212400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:75202800-75205800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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