Variant report

Variant	rs4718534
Chromosome Location	chr7:66805146-66805147
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66805031..66806726-chr7:66806842..66808833,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STAG3L4-1	chr7:66804437-66805349	XLOC_006138
2	lnc-STAG3L4-1	chr7:66804784-66805315	XLOC_006138
3	lnc-STAG3L4-1	chr7:66804223-66805449	NONHSAT121277

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11533886	0.84[EUR][1000 genomes]
rs11543606	0.84[EUR][1000 genomes]
rs11760794	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11760843	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760899	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11762397	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763894	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11765091	0.82[EUR][1000 genomes]
rs11768598	0.92[ASN][1000 genomes]
rs11769438	0.88[ASN][1000 genomes]
rs11770307	0.89[ASN][1000 genomes]
rs11771920	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772041	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772331	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773173	1.00[ASN][1000 genomes]
rs12698575	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226941	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241524	1.00[ASN][1000 genomes]
rs13241865	1.00[ASN][1000 genomes]
rs17137359	1.00[ASN][1000 genomes]
rs1968150	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33999667	0.88[AFR][1000 genomes]
rs34037266	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34167872	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34671876	1.00[ASN][1000 genomes]
rs35307336	0.95[ASN][1000 genomes]
rs35565843	0.93[ASN][1000 genomes]
rs35715970	0.97[ASN][1000 genomes]
rs36146582	0.92[ASN][1000 genomes]
rs4140690	0.83[EUR][1000 genomes]
rs4236211	0.90[ASN][1000 genomes]
rs4590320	0.89[ASN][1000 genomes]
rs4717364	1.00[ASN][1000 genomes]
rs4718536	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718559	0.87[ASN][1000 genomes]
rs4718560	0.81[ASN][1000 genomes]
rs55777645	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466443	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466454	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62467577	0.93[ASN][1000 genomes]
rs6956666	0.93[ASN][1000 genomes]
rs6960865	1.00[ASN][1000 genomes]
rs6963583	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71565103	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71565104	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7341400	0.97[ASN][1000 genomes]
rs7786846	0.92[ASN][1000 genomes]
rs7788177	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804093	0.92[ASN][1000 genomes]
rs7804537	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs887715	0.98[ASN][1000 genomes]
rs9443	1.00[ASN][1000 genomes]
rs956523	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4718534	RP11-166O4.5	cis	Muscle Skeletal	GTEx
rs4718534	TYW1	cis	Heart Left Ventricle	GTEx
rs4718534	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs4718534	STAG3L4	cis	lung	GTEx
rs4718534	STAG3L4	cis	Muscle Skeletal	GTEx
rs4718534	STAG3L4	cis	Adipose Subcutaneous	GTEx
rs4718534	STAG3L4	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66775200-66807600	Weak transcription	Colonic Mucosa	Colon
2	chr7:66777200-66805200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:66778800-66809000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:66779800-66807600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:66780400-66808200	Weak transcription	GM12878-XiMat	blood
6	chr7:66780400-66809400	Weak transcription	A549	lung
7	chr7:66781400-66810200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:66782800-66809400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:66785800-66808200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:66785800-66816200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:66786000-66809400	Weak transcription	Dnd41	blood
12	chr7:66786200-66806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr7:66786200-66809400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:66786400-66807200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr7:66786800-66809400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:66791800-66807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:66799400-66806800	Weak transcription	Primary B cells from cord blood	blood
18	chr7:66799400-66808200	Weak transcription	Fetal Lung	lung
19	chr7:66800000-66808400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr7:66800400-66808000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:66800600-66806800	Weak transcription	Right Ventricle	heart
22	chr7:66801000-66808600	Weak transcription	Aorta	Aorta
23	chr7:66801000-66809200	Weak transcription	Esophagus	oesophagus
24	chr7:66801200-66807000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:66801200-66812000	Weak transcription	Gastric	stomach
26	chr7:66802000-66809000	Weak transcription	NHEK	skin
27	chr7:66802400-66808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:66802400-66808600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:66802600-66809600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:66802600-66811800	Weak transcription	Stomach Mucosa	stomach
31	chr7:66802800-66814800	Weak transcription	HSMMtube	muscle
32	chr7:66803200-66807200	Weak transcription	HepG2	liver
33	chr7:66803200-66811600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:66803400-66809000	Weak transcription	Colon Smooth Muscle	Colon
35	chr7:66803800-66805200	Strong transcription	Liver	Liver
36	chr7:66804200-66806200	Weak transcription	Fetal Kidney	kidney
37	chr7:66804400-66805200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr7:66804400-66805200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr7:66804400-66805200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr7:66804400-66805200	Strong transcription	Fetal Brain Female	brain
41	chr7:66804400-66805200	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr7:66804400-66805400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr7:66804400-66805400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
44	chr7:66804400-66805800	Strong transcription	Left Ventricle	heart
45	chr7:66804400-66806200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:66804400-66806800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr7:66804400-66807000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:66804400-66807000	Strong transcription	Fetal Intestine Small	intestine
49	chr7:66804400-66807200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:66804400-66807200	Strong transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links