Variant report

Variant	rs210605
Chromosome Location	chr7:69235712-69235713
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1003404	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10260553	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487947	0.87[ASN][1000 genomes]
rs12670658	0.92[ASN][1000 genomes]
rs1548748	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1990444	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210602	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215354	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533436	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2533437	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851486	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851493	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2851519	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851520	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34701787	0.87[ASN][1000 genomes]
rs41848	0.92[ASN][1000 genomes]
rs41854	0.92[ASN][1000 genomes]
rs41857	0.92[ASN][1000 genomes]
rs4717522	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548556	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569334	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628885	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953849	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs917617	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3394718	chr7:69194534-69238432	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1027399	chr7:69197011-69239721	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv538918	chr7:69197011-69239721	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs210605	STAG3L4	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69217400-69237400	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:69225200-69238800	Weak transcription	Primary B cells from cord blood	blood
3	chr7:69227200-69237000	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:69229800-69238600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:69230200-69236000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:69230400-69237400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:69231000-69237800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:69232400-69237400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:69233600-69240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:69233800-69235800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:69233800-69236200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr7:69233800-69236200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:69234000-69235800	Enhancers	Brain Germinal Matrix	brain
14	chr7:69234000-69238600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:69234000-69238800	Weak transcription	Left Ventricle	heart
16	chr7:69234200-69238600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:69234400-69235800	Enhancers	GM12878-XiMat	blood
18	chr7:69234400-69236200	Enhancers	Fetal Stomach	stomach
19	chr7:69234600-69237400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:69234600-69238400	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:69234800-69236200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:69234800-69236400	Weak transcription	Ovary	ovary
23	chr7:69234800-69238000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:69234800-69238600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:69234800-69238600	Weak transcription	Pancreas	Pancrea
26	chr7:69234800-69245800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:69235000-69237000	Weak transcription	Adipose Nuclei	Adipose
28	chr7:69235000-69238200	Weak transcription	Brain Substantia Nigra	brain
29	chr7:69235000-69238600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:69235000-69238600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:69235200-69237000	Weak transcription	Fetal Lung	lung
32	chr7:69235200-69237800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:69235400-69236600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr7:69235600-69236200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr7:69235600-69236200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr7:69235600-69236200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr7:69235600-69236600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr7:69235600-69238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:69235600-69238600	Weak transcription	Fetal Heart	heart

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