Variant report

Variant	rs3864408
Chromosome Location	chr7:66785634-66785635
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1808293	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2537522	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4717365	0.91[EUR][1000 genomes];0.89[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	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
5	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
6	nsv970873	chr7:66785229-66793852	Weak transcription Strong transcription Enhancers Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3864408	STAG3L4	cis	Muscle Skeletal	GTEx
rs3864408	STAG3L4	cis	Thyroid	GTEx
rs3864408	STAG3L4	cis	Skin Sun Exposed Lower leg	GTEx
rs3864408	STAG3L4	cis	Whole Blood	GTEx
rs3864408	STAG3L4	cis	Heart Left Ventricle	GTEx
rs3864408	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs3864408	STAG3L4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
5	chr7:66770800-66786800	Strong transcription	Liver	Liver
6	chr7:66771000-66785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:66771800-66786000	Strong transcription	Fetal Intestine Large	intestine
8	chr7:66771800-66786200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr7:66772200-66786200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:66772600-66786200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr7:66774200-66785800	Weak transcription	Stomach Mucosa	stomach
12	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
13	chr7:66775600-66786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:66775800-66786400	Weak transcription	NHLF	lung
15	chr7:66777000-66786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:66777200-66789400	Weak transcription	NHDF-Ad	bronchial
17	chr7:66777200-66805200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:66777400-66787000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:66777600-66786200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:66777600-66786600	Weak transcription	HMEC	breast
21	chr7:66778400-66787200	Weak transcription	Pancreas	Pancrea
22	chr7:66778800-66809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:66779000-66787200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:66779600-66786600	Weak transcription	HSMM	muscle
25	chr7:66779800-66807600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:66780000-66786800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:66780200-66786800	Weak transcription	Osteobl	bone
28	chr7:66780200-66788800	Weak transcription	Aorta	Aorta
29	chr7:66780400-66787000	Weak transcription	K562	blood
30	chr7:66780400-66788200	Weak transcription	NHEK	skin
31	chr7:66780400-66790800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:66780400-66791000	Weak transcription	Primary B cells from cord blood	blood
33	chr7:66780400-66791800	Weak transcription	Fetal Lung	lung
34	chr7:66780400-66804600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:66780400-66808200	Weak transcription	GM12878-XiMat	blood
36	chr7:66780400-66809400	Weak transcription	A549	lung
37	chr7:66781200-66804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:66781400-66788400	Weak transcription	Gastric	stomach
39	chr7:66781400-66788800	Weak transcription	Esophagus	oesophagus
40	chr7:66781400-66792200	Weak transcription	Brain Germinal Matrix	brain
41	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:66781800-66786000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:66782200-66788200	Weak transcription	Ovary	ovary
44	chr7:66782600-66804600	Weak transcription	Brain Substantia Nigra	brain
45	chr7:66782800-66787800	Weak transcription	Thymus	Thymus
46	chr7:66782800-66788200	Weak transcription	Lung	lung
47	chr7:66782800-66788600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:66782800-66791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:66782800-66804400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:66782800-66804400	Weak transcription	Rectal Mucosa Donor 31	rectum

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