Variant report

Variant	rs2960961
Chromosome Location	chr7:66583991-66583992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10215275	0.80[AMR][1000 genomes]
rs10224228	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10224763	0.80[AMR][1000 genomes]
rs10227884	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10228157	0.88[AFR][1000 genomes]
rs10230954	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10232929	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10233035	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10234659	0.89[AFR][1000 genomes]
rs10235308	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10236844	0.94[AFR][1000 genomes]
rs10240501	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10241334	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10241454	0.93[AFR][1000 genomes]
rs10242919	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10248168	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10256861	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10271230	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10271388	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10273294	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10274048	0.91[AFR][1000 genomes]
rs10274443	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10274580	0.80[AMR][1000 genomes]
rs10277094	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10282273	0.86[AFR][1000 genomes]
rs11760968	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11763486	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11764514	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11765279	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11765283	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11765422	0.94[AFR][1000 genomes]
rs11765443	0.93[AFR][1000 genomes]
rs11766419	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11766490	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11769645	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11769928	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11769985	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11773128	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12531934	0.82[AFR][1000 genomes]
rs13222146	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13223029	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13232027	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13243892	0.82[AMR][1000 genomes]
rs13437766	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13437823	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13438033	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs17137288	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17144710	0.82[AMR][1000 genomes]
rs17144722	0.92[AFR][1000 genomes]
rs17144733	0.82[AMR][1000 genomes]
rs2140564	0.80[AMR][1000 genomes]
rs2140565	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2687060	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2690147	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2690151	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28380726	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs28760321	0.86[AFR][1000 genomes]
rs28888140	0.82[AMR][1000 genomes]
rs2949148	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2960970	0.80[AMR][1000 genomes]
rs34450608	0.91[AFR][1000 genomes]
rs34512474	0.86[AFR][1000 genomes]
rs3807368	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3962073	0.91[AFR][1000 genomes]
rs4109495	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs55647442	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55738075	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs55829112	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs55849420	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs55940282	0.90[AFR][1000 genomes]
rs56106251	0.84[AFR][1000 genomes]
rs56166786	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56307114	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs56347390	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56922729	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs57885730	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs58440009	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58723885	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58756282	0.83[AMR][1000 genomes]
rs59715913	0.87[AFR][1000 genomes]
rs59734986	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59737217	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60204091	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60800157	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6460319	0.84[AFR][1000 genomes]
rs6460321	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6460322	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6460324	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6460325	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6460326	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6460327	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6460328	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs66744554	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs66755920	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6949990	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6950170	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6950847	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6951192	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6954526	0.94[AFR][1000 genomes]
rs6959635	0.94[AFR][1000 genomes]
rs6962222	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6973836	0.80[AMR][1000 genomes]
rs71523750	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs71563164	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs71563165	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7784267	0.90[AFR][1000 genomes]
rs7787691	0.88[AFR][1000 genomes]
rs7794497	0.84[AFR][1000 genomes]
rs7800350	0.80[AMR][1000 genomes]
rs7801361	0.86[AFR][1000 genomes]
rs7809810	0.88[AFR][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	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv966838	chr7:66548076-66617503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1802655	chr7:66576034-66634666	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv1816643	chr7:66576034-66634666	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	esv1840497	chr7:66576034-66634666	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	esv1851064	chr7:66576034-66634666	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2960961	TYW1	cis	Muscle Skeletal	GTEx
rs2960961	TYW1	cis	Esophagus Mucosa	GTEx
rs2960961	TYW1	cis	Heart Left Ventricle	GTEx
rs2960961	TYW1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
2	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:66526400-66585600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:66532400-66587600	Weak transcription	Fetal Kidney	kidney
5	chr7:66533800-66623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:66535600-66593600	Weak transcription	Hela-S3	cervix
7	chr7:66538400-66593600	Weak transcription	Fetal Thymus	thymus
8	chr7:66538400-66594200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:66538400-66595800	Weak transcription	Brain Substantia Nigra	brain
10	chr7:66540800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:66543400-66600000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:66544600-66592600	Weak transcription	HepG2	liver
13	chr7:66545600-66616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:66547000-66594200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:66547600-66594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:66547600-66594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:66547800-66593400	Weak transcription	Pancreas	Pancrea
18	chr7:66547800-66602800	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:66549800-66585000	Weak transcription	Esophagus	oesophagus
20	chr7:66550000-66586200	Weak transcription	Left Ventricle	heart
21	chr7:66550000-66587800	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:66550000-66593400	Weak transcription	Spleen	Spleen
23	chr7:66550000-66624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:66550200-66584000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:66550200-66593200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr7:66554600-66595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:66555800-66587400	Weak transcription	Primary B cells from cord blood	blood
28	chr7:66560400-66593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:66560800-66589200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:66562800-66593600	Weak transcription	NHEK	skin
31	chr7:66563000-66585600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:66564800-66594400	Weak transcription	NH-A	brain
33	chr7:66565200-66589800	Weak transcription	Aorta	Aorta
34	chr7:66566400-66585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:66566400-66585400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:66566400-66587400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:66566400-66587600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:66566400-66593400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:66566400-66605600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:66566600-66593400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:66566800-66594000	Weak transcription	Lung	lung
42	chr7:66567000-66593000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:66568800-66594200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:66570600-66595800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:66570800-66591000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:66570800-66592800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:66570800-66592800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr7:66570800-66593400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:66570800-66595400	Weak transcription	Ovary	ovary
50	chr7:66571000-66584000	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links