Variant report

Variant	rs12698523
Chromosome Location	chr7:65968113-65968114
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65957205..65961212-chr7:65965422..65969556,4	K562	blood:
2	chr7:65957371..65960292-chr7:65968107..65970885,2	MCF-7	breast:
3	chr7:65967192..65970542-chr7:65973733..65976638,3	MCF-7	breast:
4	chr7:65957063..65960657-chr7:65965998..65969796,7	K562	blood:
5	chr7:65962598..65964845-chr7:65967128..65969583,2	K562	blood:

Variant related genes	Relation type
ENSG00000234500	Chromatin interaction
ENSG00000223473	Chromatin interaction
ENSG00000237310	Chromatin interaction

Extended variants
information (count: 140 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1002053	0.82[EUR][1000 genomes]
rs10215948	0.81[EUR][1000 genomes]
rs10257427	0.81[EUR][1000 genomes]
rs10267430	0.81[EUR][1000 genomes]
rs10278816	0.84[AFR][1000 genomes]
rs10281080	0.82[AFR][1000 genomes]
rs10755833	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950041	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950044	0.81[AFR][1000 genomes]
rs11763189	0.81[AMR][1000 genomes]
rs11765965	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11773628	0.81[AMR][1000 genomes]
rs12532998	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533585	0.85[AFR][1000 genomes]
rs12533997	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535036	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12668936	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12673810	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698520	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12698521	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12698532	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12698534	0.85[AFR][1000 genomes]
rs13224319	0.82[AFR][1000 genomes]
rs13227219	0.82[ASN][1000 genomes]
rs13309022	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363055	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1544549	0.80[EUR][1000 genomes]
rs1695815	0.82[EUR][1000 genomes]
rs1807064	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1833495	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1968225	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974769	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1981798	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1981799	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036264	0.82[EUR][1000 genomes]
rs2042133	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2077593	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2161065	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173570	0.80[EUR][1000 genomes]
rs2277911	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302918	0.83[AFR][1000 genomes]
rs2420591	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2420599	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2420820	0.80[EUR][1000 genomes]
rs28698552	0.81[AFR][1000 genomes]
rs2901209	0.80[AMR][1000 genomes]
rs34406470	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35149210	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35410151	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3735148	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857684	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857686	0.80[AFR][1000 genomes]
rs3898855	0.82[AFR][1000 genomes]
rs3935391	0.81[EUR][1000 genomes]
rs3981131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4717292	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4717299	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4717300	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718343	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718344	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718349	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4718357	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4718358	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55748098	0.81[EUR][1000 genomes]
rs57739047	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60193905	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62465434	0.82[AFR][1000 genomes]
rs6460291	0.82[EUR][1000 genomes]
rs6460292	0.82[EUR][1000 genomes]
rs6460295	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6460296	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460300	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6460304	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6945019	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6945032	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945775	0.81[AMR][1000 genomes]
rs6945843	0.81[EUR][1000 genomes]
rs6949920	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6956179	0.82[EUR][1000 genomes]
rs6957199	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6958200	0.83[EUR][1000 genomes]
rs6958271	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6958277	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6961155	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6961990	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6965056	0.80[AFR][1000 genomes]
rs6967996	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6970030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6970860	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978429	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6978721	0.81[EUR][1000 genomes]
rs6979382	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs709595	0.82[EUR][1000 genomes]
rs709597	0.82[EUR][1000 genomes]
rs7781061	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7781698	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7783613	0.83[EUR][1000 genomes]
rs778682	0.81[EUR][1000 genomes]
rs778685	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778689	0.82[EUR][1000 genomes]
rs778692	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778694	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778695	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778699	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778700	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778706	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778708	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778709	0.81[EUR][1000 genomes]
rs778710	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778712	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778721	0.86[EUR][1000 genomes]
rs778723	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs778726	0.82[EUR][1000 genomes]
rs778735	0.83[EUR][1000 genomes]
rs7788984	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789554	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789768	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792762	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7799834	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7803416	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7803424	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801190	0.81[AFR][1000 genomes]
rs801216	0.84[AFR][1000 genomes]
rs801217	0.84[AFR][1000 genomes]
rs937495	0.81[EUR][1000 genomes]
rs9691480	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9791895	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9969301	0.81[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12698523	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs12698523	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs12698523	GS1-124K5.4	cis	Artery Aorta	GTEx
rs12698523	GS1-124K5.11	cis	Thyroid	GTEx
rs12698523	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs12698523	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs12698523	GS1-124K5.4	cis	Whole Blood	GTEx
rs12698523	RP4-756H11.3	cis	Artery Aorta	GTEx
rs12698523	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs12698523	RP4-756H11.3	cis	lung	GTEx
rs12698523	GTF2IRD1P1	cis	Thyroid	GTEx
rs12698523	GS1-124K5.4	cis	Stomach	GTEx
rs12698523	RNU6-96P	cis	Thyroid	GTEx
rs12698523	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12698523	RP4-756H11.3	cis	Thyroid	GTEx
rs12698523	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs12698523	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs12698523	RP4-756H11.3	cis	Artery Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65959400-65968400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:65959400-65970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:65959400-65970600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:65959400-65971000	Weak transcription	Right Atrium	heart
5	chr7:65959600-65968400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:65959600-65970800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:65959600-65970800	Weak transcription	Brain Angular Gyrus	brain
8	chr7:65959600-65970800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:65959800-65969200	Weak transcription	Fetal Intestine Small	intestine
10	chr7:65959800-65970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:65959800-65970800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:65962800-65969400	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:65967600-65969400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr7:65967800-65968400	Enhancers	HepG2	liver
15	chr7:65967800-65970800	Weak transcription	NHLF	lung
16	chr7:65968000-65968600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:65968000-65968800	Weak transcription	Pancreas	Pancrea
18	chr7:65968000-65970800	Weak transcription	Ovary	ovary

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