Variant report

Variant	rs3767962
Chromosome Location	chr1:93814411-93814412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:93813597-93814416	MCF10A-Er-Src	breast:	n/a	chr1:93814208-93814220 chr1:93814210-93814218
2	MYC	chr1:93814404-93814991	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93809993..93812925-chr1:93814019..93816976,3	MCF-7	breast:
2	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
3	chr1:93813688..93816187-chr1:93818806..93820791,2	MCF-7	breast:
4	chr1:93789973..93792752-chr1:93813733..93815451,2	K562	blood:
5	chr1:93810887..93813199-chr1:93813270..93816072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	TF binding region
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1000607	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10782957	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10782959	0.83[ASN][1000 genomes]
rs10874772	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10874773	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874777	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10874778	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1088318	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164902	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11164904	0.85[ASN][1000 genomes]
rs11164916	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11576494	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044883	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124771	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133576	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133907	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12138486	0.82[ASN][1000 genomes]
rs12139633	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12406245	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12752223	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1426318	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1535699	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1535701	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559828	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593512	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2031225	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2031226	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114273	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296558	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2391254	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2391256	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35628716	0.81[ASN][1000 genomes]
rs35915989	0.80[ASN][1000 genomes]
rs3767964	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4000699	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240966	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4847240	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847406	0.85[ASN][1000 genomes]
rs4847408	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847410	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847412	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847419	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4847420	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531514	0.81[ASN][1000 genomes]
rs535760	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs547866	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs565919	0.84[EUR][1000 genomes]
rs569414	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59417472	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602204	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs612037	0.80[EUR][1000 genomes]
rs622608	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624131	0.80[EUR][1000 genomes]
rs637646	0.81[ASN][1000 genomes]
rs6541401	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541404	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6658257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680022	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6680107	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6694508	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6703310	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs682514	0.82[ASN][1000 genomes]
rs687394	0.81[ASN][1000 genomes]
rs693737	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs698927	0.81[ASN][1000 genomes]
rs7417952	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7418101	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7512911	0.81[ASN][1000 genomes]
rs7524964	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7525248	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526112	0.85[ASN][1000 genomes]
rs7537403	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7540025	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7541304	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7547244	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551485	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs771458	0.81[ASN][1000 genomes]
rs771462	0.81[ASN][1000 genomes]
rs797666	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs797668	0.84[EUR][1000 genomes]
rs797672	0.81[ASN][1000 genomes]
rs797676	0.81[EUR][1000 genomes]
rs797681	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs942196	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9432453	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432459	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9432465	0.87[ASN][1000 genomes]
rs9432681	0.82[EUR][1000 genomes];0.87[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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3767962	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs3767962	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs3767962	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs3767962	RP4-717I23.3	cis	Thyroid	GTEx
rs3767962	RP4-717I23.3	cis	lung	GTEx
rs3767962	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs3767962	DR1	cis	multi-tissue	Pritchard
rs3767962	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs3767962	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs3767962	RP4-717I23.3	cis	Artery Tibial	GTEx
rs3767962	DR1	cis	Adipose Subcutaneous	GTEx
rs3767962	RP4-717I23.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93809800-93817200	Active TSS	GM12878-XiMat	blood
2	chr1:93810000-93815400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:93810200-93815600	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:93810400-93814800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:93810400-93814800	Active TSS	Osteobl	bone
6	chr1:93810400-93815000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:93810400-93815000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:93810400-93815000	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:93810400-93815000	Active TSS	A549	lung
10	chr1:93810400-93815200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:93810400-93815200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:93810400-93815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:93810400-93815200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:93810400-93815200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:93810400-93815200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:93810400-93815200	Active TSS	K562	blood
17	chr1:93810400-93815200	Active TSS	NHLF	lung
18	chr1:93810400-93815400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:93810400-93815400	Active TSS	Fetal Intestine Large	intestine
20	chr1:93810400-93815400	Active TSS	HSMM	muscle
21	chr1:93810400-93815600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:93810400-93815600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:93810400-93815600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:93810400-93816200	Active TSS	HSMMtube	muscle
25	chr1:93810600-93814600	Active TSS	Fetal Brain Female	brain
26	chr1:93810600-93814600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:93810600-93814800	Active TSS	Brain Germinal Matrix	brain
28	chr1:93810600-93815200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:93810600-93815200	Active TSS	Fetal Stomach	stomach
30	chr1:93810600-93815200	Active TSS	NHDF-Ad	bronchial
31	chr1:93810600-93815600	Active TSS	Fetal Muscle Leg	muscle
32	chr1:93810600-93815600	Active TSS	Fetal Thymus	thymus
33	chr1:93810600-93815600	Active TSS	Right Atrium	heart
34	chr1:93810600-93815800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:93810600-93815800	Active TSS	Thymus	Thymus
36	chr1:93810800-93814600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:93810800-93814800	Active TSS	Colon Smooth Muscle	Colon
38	chr1:93810800-93815000	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr1:93810800-93815200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:93810800-93815200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr1:93810800-93815200	Active TSS	Fetal Kidney	kidney
42	chr1:93810800-93815400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:93810800-93815400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:93810800-93815400	Active TSS	Aorta	Aorta
45	chr1:93810800-93815400	Active TSS	NHEK	skin
46	chr1:93810800-93815600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr1:93810800-93815800	Active TSS	HMEC	breast
48	chr1:93811000-93815200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:93811200-93814800	Active TSS	NH-A	brain
50	chr1:93811600-93816600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links