Variant report

Variant	rs7807630
Chromosome Location	chr7:66766460-66766461
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	POLR2A	chr7:66765624-66768309	GM12878	blood:	n/a	n/a
2	MAX	chr7:66766181-66766561	K562	blood:	n/a	n/a
3	POLR2A	chr7:66766408-66768394	GM12878	blood:	n/a	n/a
4	ZNF384	chr7:66766087-66766770	K562	blood:	n/a	n/a

Variant related genes	Relation type
STAG3L4	TF binding region
ENSG00000201565	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1045513	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10807709	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13244247	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041575	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28615085	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57522994	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7791024	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7804553	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9647884	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9647886	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv8129	chr7:66735416-66766669	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv13926	chr7:66735980-66767830	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv970872	chr7:66742783-66776118	Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7807630	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs7807630	STAG3L4	cis	Nerve Tibial	GTEx
rs7807630	STAG3L4	cis	Whole Blood	GTEx
rs7807630	STAG3L4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66694800-66766600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:66701600-66766600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr7:66728600-66766600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:66729000-66767000	Weak transcription	Gastric	stomach
5	chr7:66733200-66766600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:66733400-66766800	Weak transcription	Lung	lung
7	chr7:66736400-66766600	Weak transcription	Brain Substantia Nigra	brain
8	chr7:66742600-66766800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:66747600-66766600	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:66748200-66766800	Weak transcription	Ovary	ovary
11	chr7:66749600-66766600	Weak transcription	Brain Anterior Caudate	brain
12	chr7:66749600-66766600	Weak transcription	Fetal Intestine Large	intestine
13	chr7:66751000-66766600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:66751000-66767000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:66754000-66766600	Weak transcription	Left Ventricle	heart
16	chr7:66754600-66766600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:66756600-66766600	Weak transcription	Fetal Intestine Small	intestine
18	chr7:66756600-66766600	Weak transcription	Fetal Stomach	stomach
19	chr7:66757400-66766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:66763600-66766600	Weak transcription	Primary B cells from cord blood	blood
21	chr7:66765400-66766600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:66765600-66766800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:66765800-66767000	Enhancers	Small Intestine	intestine
24	chr7:66765800-66769000	Active TSS	K562	blood
25	chr7:66766200-66766600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr7:66766200-66766600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:66766200-66766600	Enhancers	Liver	Liver
28	chr7:66766200-66766600	Enhancers	Colonic Mucosa	Colon
29	chr7:66766200-66766600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr7:66766200-66766600	Enhancers	Fetal Muscle Leg	muscle
31	chr7:66766200-66766600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr7:66766200-66766800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr7:66766200-66766800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr7:66766200-66766800	Enhancers	Placenta	Placenta
35	chr7:66766200-66767000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:66766200-66767000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:66766200-66767000	Enhancers	Spleen	Spleen
38	chr7:66766200-66768600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:66766200-66768800	Active TSS	Hela-S3	cervix
40	chr7:66766200-66769200	Active TSS	GM12878-XiMat	blood
41	chr7:66766400-66766600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr7:66766400-66766600	Enhancers	Primary T cells from cord blood	blood
43	chr7:66766400-66766600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr7:66766400-66766600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr7:66766400-66766600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr7:66766400-66766600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:66766400-66766600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:66766400-66766600	Enhancers	Adipose Nuclei	Adipose
49	chr7:66766400-66766600	Enhancers	Brain Cingulate Gyrus	brain
50	chr7:66766400-66766600	Enhancers	Brain Germinal Matrix	brain

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