Variant report

Variant	rs3980714
Chromosome Location	chr7:66519848-66519849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10081382	1.00[ASN][1000 genomes]
rs10228308	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs10238245	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs10240542	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242790	0.81[YRI][hapmap]
rs10243730	1.00[ASN][1000 genomes]
rs10247355	1.00[ASN][1000 genomes]
rs10264939	1.00[ASN][1000 genomes]
rs10266985	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10268701	0.81[YRI][hapmap]
rs13222551	1.00[ASN][1000 genomes]
rs13222852	1.00[ASN][1000 genomes]
rs13222880	1.00[ASN][1000 genomes]
rs13239441	1.00[ASN][1000 genomes]
rs13241749	1.00[ASN][1000 genomes]
rs13246453	1.00[ASN][1000 genomes]
rs2421427	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524910	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28828435	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28875922	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901443	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34208798	0.85[AFR][1000 genomes]
rs35175278	1.00[ASN][1000 genomes]
rs35955950	1.00[ASN][1000 genomes]
rs3980761	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56224758	1.00[ASN][1000 genomes]
rs56259510	1.00[ASN][1000 genomes]
rs57571665	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948594	0.83[EUR][1000 genomes]
rs6956400	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958056	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968898	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973163	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780458	0.85[YRI][hapmap]
rs7783776	1.00[ASN][1000 genomes]
rs7789673	1.00[ASN][1000 genomes]
rs7791848	1.00[ASN][1000 genomes]
rs7795025	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797194	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809602	1.00[ASN][1000 genomes]
rs7811073	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9654770	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9691420	1.00[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	nsv981515	chr7:66477535-66532313	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3980714	TYW1	cis	Muscle Skeletal	GTEx
rs3980714	ZNF117	cis	parietal	SCAN
rs3980714	ERV3	cis	parietal	SCAN
rs3980714	ERV3	cis	cerebellum	SCAN
rs3980714	TYW1	cis	Esophagus Mucosa	GTEx
rs3980714	ZNF117	cis	cerebellum	SCAN
rs3980714	ASL	cis	cerebellum	SCAN
rs3980714	TYW1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66483400-66551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:66483600-66534400	Weak transcription	Aorta	Aorta
3	chr7:66486400-66531600	Weak transcription	Ovary	ovary
4	chr7:66487000-66576600	Weak transcription	Gastric	stomach
5	chr7:66495000-66532200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:66495200-66523000	Weak transcription	Esophagus	oesophagus
7	chr7:66495200-66523600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:66495200-66538000	Weak transcription	Brain Germinal Matrix	brain
9	chr7:66495200-66539400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
11	chr7:66495400-66529600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:66495400-66531800	Weak transcription	Fetal Kidney	kidney
13	chr7:66495400-66533200	Weak transcription	Thymus	Thymus
14	chr7:66495400-66534400	Weak transcription	Spleen	Spleen
15	chr7:66495600-66532200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:66495600-66533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:66495600-66547400	Weak transcription	Pancreas	Pancrea
18	chr7:66498600-66534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:66498600-66549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr7:66500200-66525000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:66501000-66522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:66501000-66540000	Weak transcription	Psoas Muscle	Psoas
23	chr7:66502400-66534400	Weak transcription	Lung	lung
24	chr7:66502400-66549600	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:66506600-66534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:66508000-66532200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:66508000-66533400	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:66508400-66522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:66508800-66520000	Weak transcription	Fetal Heart	heart
30	chr7:66508800-66528800	Weak transcription	Brain Anterior Caudate	brain
31	chr7:66508800-66533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:66508800-66533800	Weak transcription	Hela-S3	cervix
33	chr7:66508800-66537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:66508800-66538000	Weak transcription	A549	lung
35	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:66509000-66523000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:66509000-66527400	Weak transcription	HSMMtube	muscle
38	chr7:66509000-66531200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:66509000-66531200	Weak transcription	Osteobl	bone
40	chr7:66509000-66533200	Weak transcription	HSMM	muscle
41	chr7:66509000-66538000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:66509000-66539600	Weak transcription	HMEC	breast
43	chr7:66509400-66533000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:66509400-66536600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr7:66510800-66532000	Weak transcription	K562	blood
46	chr7:66511200-66537600	Weak transcription	Brain Substantia Nigra	brain
47	chr7:66511400-66539800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:66512000-66529200	Weak transcription	Primary B cells from cord blood	blood
49	chr7:66512000-66531600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:66512400-66535000	Weak transcription	Colonic Mucosa	Colon

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