Variant report

Variant	rs2901209
Chromosome Location	chr7:65984923-65984924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10107	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10274883	0.81[EUR][1000 genomes]
rs10278014	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10807704	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950043	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11763189	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11764589	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11765791	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11769079	0.80[EUR][1000 genomes]
rs11773628	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12333370	0.83[EUR][1000 genomes]
rs12532998	0.81[AMR][1000 genomes]
rs12668005	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12673450	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12698522	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12698523	0.80[AMR][1000 genomes]
rs12698526	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12698532	0.83[AMR][1000 genomes]
rs13226170	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13232191	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13240501	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13242290	0.81[EUR][1000 genomes]
rs13309022	0.81[AMR][1000 genomes]
rs13536	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1643375	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17747530	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1860469	0.83[EUR][1000 genomes]
rs1860472	0.83[EUR][1000 genomes]
rs1968126	0.81[EUR][1000 genomes]
rs2013908	0.81[EUR][1000 genomes]
rs2024192	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2109295	0.83[EUR][1000 genomes]
rs2109297	0.81[EUR][1000 genomes]
rs2420608	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420610	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420611	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2659907	0.80[EUR][1000 genomes]
rs2659908	0.80[EUR][1000 genomes]
rs28480509	0.82[EUR][1000 genomes]
rs28714531	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28731376	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35378740	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3735148	0.80[AMR][1000 genomes]
rs3846973	0.81[EUR][1000 genomes]
rs3857685	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3926380	0.83[EUR][1000 genomes]
rs4718356	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718358	0.83[AFR][1000 genomes]
rs4718377	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4718383	0.82[EUR][1000 genomes]
rs57739047	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61348003	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6460301	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6460302	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6460303	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6460304	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66981195	0.82[EUR][1000 genomes]
rs6945775	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951302	0.80[EUR][1000 genomes]
rs6951946	0.86[EUR][1000 genomes]
rs6955837	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6957199	0.82[AMR][1000 genomes]
rs6958271	0.81[AMR][1000 genomes]
rs6958277	0.81[AMR][1000 genomes]
rs6962717	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6970030	0.80[AMR][1000 genomes]
rs6970357	0.80[AMR][1000 genomes]
rs6970860	0.81[AMR][1000 genomes]
rs6971059	0.86[EUR][1000 genomes]
rs6976714	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978028	0.82[AFR][1000 genomes]
rs6978178	0.81[EUR][1000 genomes]
rs6980451	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7384021	0.84[EUR][1000 genomes]
rs7778322	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778680	0.81[EUR][1000 genomes]
rs778702	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778703	0.83[EUR][1000 genomes]
rs778715	0.82[EUR][1000 genomes]
rs778716	0.82[EUR][1000 genomes]
rs778720	0.82[EUR][1000 genomes]
rs7789615	0.82[AFR][1000 genomes]
rs7808013	0.83[EUR][1000 genomes]
rs801194	0.87[EUR][1000 genomes]
rs801195	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs801202	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs801203	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs801204	0.89[EUR][1000 genomes]
rs801206	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs801208	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs801209	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs801215	0.81[EUR][1000 genomes]
rs809025	0.83[EUR][1000 genomes]
rs881285	0.81[EUR][1000 genomes]
rs9791712	0.83[EUR][1000 genomes]
rs9791713	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1027068	chr7:65901543-65991211	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2901209	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2901209	LINC00174	cis	Thyroid	GTEx
rs2901209	GS1-124K5.11	cis	Thyroid	GTEx
rs2901209	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2901209	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2901209	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2901209	RP4-756H11.3	cis	Thyroid	GTEx
rs2901209	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2901209	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2901209	GTF2IRD1P1	cis	Thyroid	GTEx
rs2901209	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs2901209	RP4-756H11.3	cis	lung	GTEx
rs2901209	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2901209	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2901209	GS1-124K5.2	cis	Whole Blood	GTEx
rs2901209	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2901209	GS1-124K5.4	cis	Stomach	GTEx
rs2901209	RNU6-96P	cis	Thyroid	GTEx
rs2901209	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2901209	RP4-756H11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65975200-65989600	Weak transcription	Fetal Intestine Small	intestine
2	chr7:65980600-65989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:65981400-66001000	Weak transcription	Fetal Brain Female	brain
4	chr7:65982600-65989000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:65983000-65990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:65983400-66001800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:65983400-66006000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:65983600-65987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:65983600-65994400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:65983600-66000400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:65984000-65985200	Enhancers	HepG2	liver
12	chr7:65984400-65987600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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