Variant report

Variant	rs3962073
Chromosome Location	chr7:66575141-66575142
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10224228	0.93[AFR][1000 genomes]
rs10227884	0.83[AFR][1000 genomes]
rs10228157	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10230954	0.92[AFR][1000 genomes]
rs10232929	0.83[AFR][1000 genomes]
rs10233035	0.83[AFR][1000 genomes]
rs10234659	0.87[AFR][1000 genomes]
rs10235308	0.86[AFR][1000 genomes]
rs10236844	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10240501	0.93[AFR][1000 genomes]
rs10241334	0.88[AFR][1000 genomes]
rs10241454	0.85[AFR][1000 genomes]
rs10242919	0.81[AFR][1000 genomes]
rs10248168	0.87[AFR][1000 genomes]
rs10256861	0.88[AFR][1000 genomes]
rs10271230	0.93[AFR][1000 genomes]
rs10271388	0.88[AFR][1000 genomes]
rs10273294	0.92[AFR][1000 genomes]
rs10274048	0.88[AFR][1000 genomes]
rs10274443	0.92[AFR][1000 genomes]
rs10277094	0.84[AFR][1000 genomes]
rs10282273	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10950060	0.92[ASN][1000 genomes]
rs11760318	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11760968	0.90[AFR][1000 genomes]
rs11763486	0.87[AFR][1000 genomes]
rs11764514	0.93[AFR][1000 genomes]
rs11765279	0.87[AFR][1000 genomes]
rs11765283	0.87[AFR][1000 genomes]
rs11765422	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11765443	0.95[AFR][1000 genomes]
rs11766419	0.86[AFR][1000 genomes]
rs11766490	0.94[AFR][1000 genomes]
rs11769645	0.83[AFR][1000 genomes]
rs11769928	0.94[AFR][1000 genomes]
rs11769985	0.86[AFR][1000 genomes]
rs11773128	0.93[AFR][1000 genomes]
rs12531934	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12537557	0.86[ASN][1000 genomes]
rs13222146	0.94[AFR][1000 genomes]
rs13223029	0.91[AFR][1000 genomes]
rs13232027	0.91[AFR][1000 genomes]
rs13437766	0.81[AFR][1000 genomes]
rs13437823	0.92[AFR][1000 genomes]
rs13438033	0.92[AFR][1000 genomes]
rs17137288	0.87[AFR][1000 genomes]
rs17144722	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2140565	0.92[AFR][1000 genomes]
rs2421287	0.81[ASN][1000 genomes]
rs2687060	0.85[AFR][1000 genomes]
rs2690147	0.89[AFR][1000 genomes]
rs2690151	0.84[AFR][1000 genomes]
rs28380726	0.87[AFR][1000 genomes]
rs28760321	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2949148	0.94[AFR][1000 genomes]
rs2960961	0.91[AFR][1000 genomes]
rs34450608	0.86[AFR][1000 genomes]
rs34512474	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34787423	0.85[ASN][1000 genomes]
rs35644973	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3807368	0.86[AFR][1000 genomes]
rs4109495	0.91[AFR][1000 genomes]
rs4717347	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4718452	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs55647442	0.83[AFR][1000 genomes]
rs55738075	0.90[AFR][1000 genomes]
rs55829112	0.87[AFR][1000 genomes]
rs55849420	0.83[AFR][1000 genomes]
rs55940282	0.88[AFR][1000 genomes]
rs55958146	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56166786	0.85[AFR][1000 genomes]
rs56243158	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56307114	0.84[AFR][1000 genomes]
rs56347390	0.94[AFR][1000 genomes]
rs56922729	0.80[AFR][1000 genomes]
rs57885730	0.92[AFR][1000 genomes]
rs58440009	0.89[AFR][1000 genomes]
rs58723885	0.85[AFR][1000 genomes]
rs59715913	0.87[AFR][1000 genomes]
rs59734986	0.82[AFR][1000 genomes]
rs59737217	0.85[AFR][1000 genomes]
rs60204091	0.94[AFR][1000 genomes]
rs60356903	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60800157	0.86[AFR][1000 genomes]
rs6460319	0.82[AFR][1000 genomes]
rs6460321	0.82[AFR][1000 genomes]
rs6460322	0.94[AFR][1000 genomes]
rs6460324	0.86[AFR][1000 genomes]
rs6460325	0.80[AFR][1000 genomes]
rs6460328	0.80[AFR][1000 genomes]
rs66744554	0.82[AFR][1000 genomes]
rs66755920	0.85[AFR][1000 genomes]
rs6950170	0.94[AFR][1000 genomes]
rs6950847	0.85[AFR][1000 genomes]
rs6951192	0.93[AFR][1000 genomes]
rs6954526	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6959635	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6962222	0.86[AFR][1000 genomes]
rs71523750	0.87[AFR][1000 genomes]
rs71563164	0.88[AFR][1000 genomes]
rs71563165	0.80[AFR][1000 genomes]
rs7783888	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7784267	0.88[AFR][1000 genomes]
rs7787691	0.87[AFR][1000 genomes]
rs7794060	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7794497	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7801361	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7809810	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9654849	0.84[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	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3962073	GS1-124K5.4	cis	Nerve Tibial	GTEx
rs3962073	TYW1	cis	Muscle Skeletal	GTEx
rs3962073	TYW1	cis	Heart Left Ventricle	GTEx
rs3962073	TYW1	Cis_1M	lymphoblastoid	RTeQTL
rs3962073	TYW1	cis	Esophagus Mucosa	GTEx
rs3962073	TYW1	cis	Nerve Tibial	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66487000-66576600	Weak transcription	Gastric	stomach
2	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
3	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:66526400-66585600	Weak transcription	Brain Angular Gyrus	brain
5	chr7:66532400-66587600	Weak transcription	Fetal Kidney	kidney
6	chr7:66532600-66582800	Weak transcription	HSMMtube	muscle
7	chr7:66533800-66623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr7:66534000-66575600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:66535600-66593600	Weak transcription	Hela-S3	cervix
10	chr7:66538400-66593600	Weak transcription	Fetal Thymus	thymus
11	chr7:66538400-66594200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:66538400-66595800	Weak transcription	Brain Substantia Nigra	brain
13	chr7:66538600-66575200	Weak transcription	Fetal Lung	lung
14	chr7:66540400-66582800	Weak transcription	Placenta	Placenta
15	chr7:66540800-66594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:66543400-66600000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:66544600-66592600	Weak transcription	HepG2	liver
18	chr7:66545600-66616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:66547000-66577400	Weak transcription	A549	lung
20	chr7:66547000-66594200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:66547600-66594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:66547600-66594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:66547800-66593400	Weak transcription	Pancreas	Pancrea
24	chr7:66547800-66602800	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:66549800-66585000	Weak transcription	Esophagus	oesophagus
26	chr7:66550000-66582800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:66550000-66586200	Weak transcription	Left Ventricle	heart
28	chr7:66550000-66587800	Weak transcription	Brain Hippocampus Middle	brain
29	chr7:66550000-66593400	Weak transcription	Spleen	Spleen
30	chr7:66550000-66624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr7:66550200-66575400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:66550200-66583600	Weak transcription	Adipose Nuclei	Adipose
33	chr7:66550200-66584000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr7:66550200-66593200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:66554600-66595000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:66555800-66587400	Weak transcription	Primary B cells from cord blood	blood
37	chr7:66558200-66575600	Weak transcription	Fetal Stomach	stomach
38	chr7:66560400-66593600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:66560800-66589200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:66561600-66579000	Weak transcription	Colon Smooth Muscle	Colon
41	chr7:66562800-66593600	Weak transcription	NHEK	skin
42	chr7:66563000-66585600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr7:66564400-66576600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:66564800-66582000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:66564800-66582800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:66564800-66594400	Weak transcription	NH-A	brain
47	chr7:66565200-66589800	Weak transcription	Aorta	Aorta
48	chr7:66566200-66583000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:66566400-66585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:66566400-66585400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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