Variant report

Variant	rs62466401
Chromosome Location	chr7:66784730-66784731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12530786	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531602	0.81[ASN][1000 genomes]
rs12532084	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534602	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535489	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12535715	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12537527	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537772	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17140742	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17144955	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17145211	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17786435	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277021	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41533347	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717368	0.80[EUR][1000 genomes]
rs4717374	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4717380	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4718526	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4718552	0.83[ASN][1000 genomes]
rs56878889	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58131305	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58757717	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60593769	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61657086	0.93[ASN][1000 genomes]
rs62466395	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62466398	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62466404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466433	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62466442	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62466449	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466450	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466451	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62467568	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467572	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62467573	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467574	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467575	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467578	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62467579	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62466401	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs62466401	STAG3L4	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66769000-66785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:66769400-66785000	Strong transcription	Fetal Stomach	stomach
3	chr7:66769400-66785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr7:66770000-66785400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:66770600-66785200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr7:66770600-66785400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
11	chr7:66770800-66786800	Strong transcription	Liver	Liver
12	chr7:66771000-66785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:66771200-66785000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:66771200-66785000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:66771400-66785600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:66771800-66786000	Strong transcription	Fetal Intestine Large	intestine
17	chr7:66771800-66786200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr7:66772200-66786200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:66772600-66785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:66772600-66786200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr7:66774200-66785800	Weak transcription	Stomach Mucosa	stomach
22	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
23	chr7:66775600-66786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:66775800-66786400	Weak transcription	NHLF	lung
25	chr7:66777000-66786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:66777200-66789400	Weak transcription	NHDF-Ad	bronchial
27	chr7:66777200-66805200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:66777400-66785400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:66777400-66787000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:66777600-66785200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:66777600-66786200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:66777600-66786600	Weak transcription	HMEC	breast
33	chr7:66778400-66787200	Weak transcription	Pancreas	Pancrea
34	chr7:66778800-66809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:66779000-66787200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:66779200-66785000	Strong transcription	Fetal Intestine Small	intestine
37	chr7:66779600-66785000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:66779600-66786600	Weak transcription	HSMM	muscle
39	chr7:66779800-66807600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:66780000-66786800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:66780200-66786800	Weak transcription	Osteobl	bone
42	chr7:66780200-66788800	Weak transcription	Aorta	Aorta
43	chr7:66780400-66787000	Weak transcription	K562	blood
44	chr7:66780400-66788200	Weak transcription	NHEK	skin
45	chr7:66780400-66790800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:66780400-66791000	Weak transcription	Primary B cells from cord blood	blood
47	chr7:66780400-66791800	Weak transcription	Fetal Lung	lung
48	chr7:66780400-66804600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr7:66780400-66808200	Weak transcription	GM12878-XiMat	blood
50	chr7:66780400-66809400	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links