Variant report

Variant	rs55748098
Chromosome Location	chr7:65763618-65763619
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	chr7:65761628..65763659-chr7:65767001..65768634,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRCP-1	chr7:65763501-65766051	l_3431_chr7:65761393-65766051_brain

Extended variants
information (count: 141 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1000464	0.82[AMR][1000 genomes]
rs1002053	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10215948	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10224872	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10240949	0.82[AMR][1000 genomes]
rs10257427	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10261398	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10267430	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10276077	0.81[AMR][1000 genomes]
rs10282433	0.80[AMR][1000 genomes]
rs10755833	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10950033	0.81[AMR][1000 genomes]
rs11760844	0.81[AMR][1000 genomes]
rs11765965	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11971949	0.80[EUR][1000 genomes]
rs11974219	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11974264	0.83[EUR][1000 genomes]
rs12532998	0.81[EUR][1000 genomes]
rs12533997	0.81[EUR][1000 genomes]
rs12535036	0.81[EUR][1000 genomes]
rs12537823	0.81[AMR][1000 genomes]
rs12668936	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12673810	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12698520	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12698521	0.83[AMR][1000 genomes]
rs12698523	0.81[EUR][1000 genomes]
rs13225383	0.83[EUR][1000 genomes]
rs13227219	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13309022	0.81[EUR][1000 genomes]
rs1363055	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1540651	0.81[EUR][1000 genomes]
rs1565531	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1643395	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1695815	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1807064	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1833495	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968225	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1974769	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036263	0.82[AMR][1000 genomes]
rs2036264	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042133	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2077593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161065	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2173570	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277911	0.81[EUR][1000 genomes]
rs2420168	0.80[EUR][1000 genomes]
rs2420591	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420599	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28682868	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34406470	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35028832	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35149210	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3735148	0.81[EUR][1000 genomes]
rs3857684	0.83[AMR][1000 genomes]
rs3935391	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3981131	0.81[EUR][1000 genomes]
rs4078376	0.84[AMR][1000 genomes]
rs4149461	0.81[AMR][1000 genomes]
rs4236208	0.80[AMR][1000 genomes]
rs4587224	0.81[AMR][1000 genomes]
rs4717292	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4717299	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4717300	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718343	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718344	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718349	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4718357	0.82[EUR][1000 genomes]
rs55962648	0.81[EUR][1000 genomes]
rs6460290	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6460291	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460292	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460295	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6460296	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460300	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6945019	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6945032	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6945843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6949920	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6956179	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6959268	0.82[AMR][1000 genomes]
rs6960476	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6961155	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6961990	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6963646	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6970030	0.80[EUR][1000 genomes]
rs6970357	0.81[EUR][1000 genomes]
rs6971509	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6971752	0.80[AMR][1000 genomes]
rs6977501	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6978429	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6978721	0.81[EUR][1000 genomes]
rs6979382	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709595	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709596	0.83[AFR][1000 genomes]
rs709597	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7781061	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7781698	0.81[EUR][1000 genomes]
rs7782704	0.82[AMR][1000 genomes]
rs7783613	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778680	0.80[AMR][1000 genomes]
rs778682	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778684	0.81[AMR][1000 genomes]
rs778685	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778689	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778692	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778694	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778695	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778699	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778700	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778706	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778708	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778709	0.85[EUR][1000 genomes]
rs778710	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778712	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778721	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778723	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778724	0.81[AMR][1000 genomes]
rs778726	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778727	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778728	0.81[AMR][1000 genomes]
rs778731	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778734	0.81[AMR][1000 genomes]
rs778735	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7788984	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7789554	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7789768	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7791891	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794930	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7799834	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7803416	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7803424	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937495	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs949930	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9691480	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9791895	0.81[EUR][1000 genomes]
rs9969301	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9986696	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs55748098	RP4-756H11.3	cis	Artery Aorta	GTEx
rs55748098	GTF2IRD1P1	cis	Thyroid	GTEx
rs55748098	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs55748098	GS1-124K5.4	cis	Artery Aorta	GTEx
rs55748098	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs55748098	RP4-756H11.3	cis	lung	GTEx
rs55748098	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs55748098	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs55748098	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs55748098	RNU6-96P	cis	Thyroid	GTEx
rs55748098	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs55748098	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs55748098	RP4-756H11.3	cis	Thyroid	GTEx
rs55748098	GS1-124K5.4	cis	Stomach	GTEx
rs55748098	GS1-124K5.4	cis	Whole Blood	GTEx
rs55748098	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs55748098	RP4-756H11.3	cis	Artery Tibial	GTEx
rs55748098	GS1-124K5.11	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65747800-65766600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:65761000-65768600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:65761600-65772400	Weak transcription	HSMM	muscle
4	chr7:65762000-65765600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:65762600-65763800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:65762600-65765200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:65762600-65768800	Weak transcription	NHLF	lung
8	chr7:65762800-65768000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:65763000-65764200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:65763000-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:65763000-65769200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:65763000-65770400	Weak transcription	HepG2	liver
13	chr7:65763000-65786200	Weak transcription	Primary B cells from cord blood	blood
14	chr7:65763200-65763800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
15	chr7:65763200-65763800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:65763200-65765200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:65763200-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:65763200-65768200	Weak transcription	NHEK	skin
19	chr7:65763200-65768800	Weak transcription	HMEC	breast
20	chr7:65763400-65764600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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