Variant report

Variant	rs1318091
Chromosome Location	chr7:66786665-66786666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10224468	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10273547	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10950071	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11765153	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11765818	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11976633	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698586	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989425	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604420	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34000470	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36108509	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4717369	0.87[ASN][1000 genomes]
rs4718532	0.94[ASN][1000 genomes]
rs4718533	0.94[ASN][1000 genomes]
rs4718535	0.94[ASN][1000 genomes]
rs4718539	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467569	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62467571	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460340	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958460	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6963760	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6967594	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6979307	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs759012	0.94[ASN][1000 genomes]
rs759013	0.94[ASN][1000 genomes]
rs7806514	0.93[ASN][1000 genomes]
rs887710	0.94[ASN][1000 genomes]
rs985435	0.85[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1318091	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs1318091	STAG3L4	cis	Whole Blood	GTEx
rs1318091	STAG3L4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:66770800-66786800	Strong transcription	Liver	Liver
3	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
4	chr7:66777200-66789400	Weak transcription	NHDF-Ad	bronchial
5	chr7:66777200-66805200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:66777400-66787000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:66778400-66787200	Weak transcription	Pancreas	Pancrea
8	chr7:66778800-66809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:66779000-66787200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:66779800-66807600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:66780000-66786800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:66780200-66786800	Weak transcription	Osteobl	bone
13	chr7:66780200-66788800	Weak transcription	Aorta	Aorta
14	chr7:66780400-66787000	Weak transcription	K562	blood
15	chr7:66780400-66788200	Weak transcription	NHEK	skin
16	chr7:66780400-66790800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:66780400-66791000	Weak transcription	Primary B cells from cord blood	blood
18	chr7:66780400-66791800	Weak transcription	Fetal Lung	lung
19	chr7:66780400-66804600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:66780400-66808200	Weak transcription	GM12878-XiMat	blood
21	chr7:66780400-66809400	Weak transcription	A549	lung
22	chr7:66781200-66804600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:66781400-66788400	Weak transcription	Gastric	stomach
24	chr7:66781400-66788800	Weak transcription	Esophagus	oesophagus
25	chr7:66781400-66792200	Weak transcription	Brain Germinal Matrix	brain
26	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr7:66782200-66788200	Weak transcription	Ovary	ovary
28	chr7:66782600-66804600	Weak transcription	Brain Substantia Nigra	brain
29	chr7:66782800-66787800	Weak transcription	Thymus	Thymus
30	chr7:66782800-66788200	Weak transcription	Lung	lung
31	chr7:66782800-66788600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:66782800-66791600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr7:66782800-66804400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:66782800-66804400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr7:66782800-66809400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:66783000-66786800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:66783000-66790000	Weak transcription	Right Ventricle	heart
38	chr7:66783000-66792000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:66783000-66804400	Weak transcription	Left Ventricle	heart
40	chr7:66783000-66804600	Weak transcription	Brain Angular Gyrus	brain
41	chr7:66783200-66789200	Weak transcription	Spleen	Spleen
42	chr7:66783200-66789800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:66783400-66787400	Weak transcription	Fetal Thymus	thymus
44	chr7:66783400-66788200	Weak transcription	Primary T cells from cord blood	blood
45	chr7:66783400-66788600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr7:66783400-66789400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:66784600-66804400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:66784800-66786800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:66784800-66804400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:66785000-66787000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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