Variant report

Variant	rs6460303
Chromosome Location	chr7:65964412-65964413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65962598..65964845-chr7:65967128..65969583,2	K562	blood:
2	chr7:65962598..65967020-chr7:65967128..65971576,5	K562	blood:

Variant related genes	Relation type
ENSG00000179342	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10107	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10228885	0.82[EUR][1000 genomes]
rs10250544	0.82[EUR][1000 genomes]
rs10257911	0.81[EUR][1000 genomes]
rs10260426	0.82[EUR][1000 genomes]
rs10263690	0.82[EUR][1000 genomes]
rs10265311	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10271548	0.80[ASN][1000 genomes]
rs10274883	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278014	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10447522	0.82[EUR][1000 genomes]
rs10807704	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1083554	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10950043	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950046	0.81[ASN][1000 genomes]
rs11763189	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11764589	0.83[EUR][1000 genomes]
rs11765791	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11772884	0.87[AMR][1000 genomes]
rs11773628	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11984115	0.82[EUR][1000 genomes]
rs12333370	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12531677	0.82[EUR][1000 genomes]
rs12668005	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673450	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698522	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12698526	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226170	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13230545	0.82[EUR][1000 genomes]
rs13232191	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240501	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13242290	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13536	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1532571	0.82[EUR][1000 genomes]
rs1643375	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17747530	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1860469	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860472	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1875057	0.82[EUR][1000 genomes]
rs1968126	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013908	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2024192	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088653	0.83[EUR][1000 genomes]
rs2088655	0.82[EUR][1000 genomes]
rs2109295	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2109297	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420599	0.82[AFR][1000 genomes]
rs2420608	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2420610	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2420611	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659907	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659908	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28431318	0.84[ASN][1000 genomes]
rs28480509	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28617601	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28714531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28731376	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2901152	0.82[EUR][1000 genomes]
rs2901209	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2909688	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35378740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3846973	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3857685	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3926380	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4506088	0.85[ASN][1000 genomes]
rs4718356	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4718358	0.83[AFR][1000 genomes]
rs4718377	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718383	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57739047	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61348003	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6460284	0.82[EUR][1000 genomes]
rs6460287	0.82[EUR][1000 genomes]
rs6460293	0.83[EUR][1000 genomes]
rs6460301	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460302	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460304	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66981195	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6945775	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6951302	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6951946	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6955837	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6958294	0.82[EUR][1000 genomes]
rs6960446	0.82[EUR][1000 genomes]
rs6961990	0.81[AFR][1000 genomes]
rs6962717	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6963228	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971059	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6973249	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6976714	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6978028	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6978178	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6979452	0.83[EUR][1000 genomes]
rs6980451	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs721717	0.88[ASN][1000 genomes]
rs7384021	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7385102	0.86[AMR][1000 genomes]
rs7778322	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7782587	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7783779	0.82[EUR][1000 genomes]
rs778690	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778697	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778702	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs778703	0.81[EUR][1000 genomes]
rs778705	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778707	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs778711	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs778715	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs778716	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs778720	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs778736	0.83[EUR][1000 genomes]
rs7788984	0.83[AFR][1000 genomes]
rs7789615	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7792762	0.83[AMR][1000 genomes]
rs7793723	0.87[ASN][1000 genomes]
rs7796162	0.81[EUR][1000 genomes]
rs7798630	0.82[EUR][1000 genomes]
rs7808013	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801194	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801195	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801202	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801203	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801204	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801206	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801208	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801209	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801215	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs809025	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs881285	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791712	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9791713	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][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
rs6460303	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6460303	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6460303	GS1-124K5.2	cis	Whole Blood	GTEx
rs6460303	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6460303	GS1-124K5.4	cis	Artery Aorta	GTEx
rs6460303	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6460303	RNU6-96P	cis	Thyroid	GTEx
rs6460303	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6460303	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6460303	LINC00174	cis	Thyroid	GTEx
rs6460303	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6460303	GS1-124K5.11	cis	Thyroid	GTEx
rs6460303	RP4-756H11.3	cis	Thyroid	GTEx
rs6460303	RP4-756H11.3	cis	lung	GTEx
rs6460303	GTF2IRD1P1	cis	Thyroid	GTEx
rs6460303	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6460303	GS1-124K5.4	cis	Stomach	GTEx
rs6460303	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6460303	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6460303	RP4-756H11.3	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65959400-65966000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:65959400-65966800	Weak transcription	Pancreas	Pancrea
3	chr7:65959400-65967400	Weak transcription	Ovary	ovary
4	chr7:65959400-65968400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:65959400-65970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:65959400-65970600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:65959400-65971000	Weak transcription	Right Atrium	heart
8	chr7:65959600-65965200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:65959600-65965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:65959600-65965800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:65959600-65966200	Weak transcription	Adipose Nuclei	Adipose
12	chr7:65959600-65966400	Weak transcription	Liver	Liver
13	chr7:65959600-65966600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:65959600-65967000	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:65959600-65968400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:65959600-65970800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:65959600-65970800	Weak transcription	Brain Angular Gyrus	brain
18	chr7:65959600-65970800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:65959800-65965200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:65959800-65965200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:65959800-65965200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr7:65959800-65966200	Weak transcription	Primary B cells from cord blood	blood
23	chr7:65959800-65966600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:65959800-65966800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:65959800-65967200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:65959800-65967400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:65959800-65969200	Weak transcription	Fetal Intestine Small	intestine
28	chr7:65959800-65970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:65959800-65970800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:65960000-65965200	Weak transcription	K562	blood
31	chr7:65960200-65965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr7:65960200-65967600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:65962600-65965200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr7:65962800-65969400	Weak transcription	Brain Hippocampus Middle	brain
35	chr7:65963400-65965200	Weak transcription	HepG2	liver

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