Variant report

Variant	rs6979307
Chromosome Location	chr7:66782481-66782482
allele	C/T
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	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10273547	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950071	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11765153	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11765818	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11976633	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12698586	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1318091	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1989425	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604420	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34000470	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36108509	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717369	0.88[ASN][1000 genomes]
rs4718532	0.96[ASN][1000 genomes]
rs4718533	0.96[ASN][1000 genomes]
rs4718535	0.96[ASN][1000 genomes]
rs4718539	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62467569	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467571	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6460340	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6958460	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963760	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6967594	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs759012	0.96[ASN][1000 genomes]
rs759013	0.96[ASN][1000 genomes]
rs7806514	0.95[ASN][1000 genomes]
rs887710	0.96[ASN][1000 genomes]
rs985435	0.84[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6979307	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs6979307	STAG3L4	cis	Esophagus Muscularis	GTEx
rs6979307	STAG3L4	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66768800-66783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:66768800-66783400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:66769000-66785400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:66769400-66782800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:66769400-66783400	Strong transcription	Primary T cells from cord blood	blood
6	chr7:66769400-66785000	Strong transcription	Fetal Stomach	stomach
7	chr7:66769400-66785600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:66770000-66782800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:66770000-66783000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr7:66770000-66783400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr7:66770000-66785400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr7:66770200-66783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:66770200-66785800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:66770400-66783400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:66770400-66783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:66770400-66783600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:66770400-66786200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:66770400-66786800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:66770600-66782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:66770600-66785200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr7:66770600-66785400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr7:66770600-66786400	Weak transcription	Fetal Heart	heart
23	chr7:66770800-66783400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:66770800-66786800	Strong transcription	Liver	Liver
25	chr7:66771000-66785800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:66771200-66785000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:66771200-66785000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:66771400-66783000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:66771400-66785600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:66771600-66783000	Strong transcription	Left Ventricle	heart
31	chr7:66771800-66783400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:66771800-66786000	Strong transcription	Fetal Intestine Large	intestine
33	chr7:66771800-66786200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:66772200-66783200	Strong transcription	Spleen	Spleen
35	chr7:66772200-66786200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:66772400-66783000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr7:66772400-66783000	Strong transcription	Dnd41	blood
38	chr7:66772400-66783600	Strong transcription	Fetal Muscle Leg	muscle
39	chr7:66772600-66785600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:66772600-66786200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:66773000-66782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:66774200-66783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:66774200-66785800	Weak transcription	Stomach Mucosa	stomach
44	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
45	chr7:66775400-66784400	Weak transcription	Psoas Muscle	Psoas
46	chr7:66775600-66786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:66775800-66786400	Weak transcription	NHLF	lung
48	chr7:66776000-66782800	Strong transcription	Thymus	Thymus
49	chr7:66777000-66786000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:66777200-66783000	Strong transcription	Right Ventricle	heart

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