Variant report

Variant	rs4718378
Chromosome Location	chr7:66049687-66049688
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66049357..66051342-chr7:66055893..66058877,2	K562	blood:
2	chr7:66049008..66051947-chr7:66055778..66057625,2	MCF-7	breast:
3	chr7:66044739..66046624-chr7:66048819..66050510,2	K562	blood:
4	chr7:66047534..66050198-chr7:66118731..66121007,2	K562	blood:
5	chr7:66047534..66050313-chr7:66118210..66120231,2	K562	blood:

Variant related genes	Relation type
ENSG00000232559	Chromatin interaction
ENSG00000226824	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10215132	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10242423	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10249404	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10253883	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10255377	0.82[AMR][1000 genomes]
rs10258739	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272357	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10278371	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10278816	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10281080	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10281646	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950044	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10950045	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11765356	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11772179	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11773829	0.80[AFR][1000 genomes]
rs12532355	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12534943	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860468	0.80[AFR][1000 genomes]
rs1968127	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28846700	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35117338	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3857686	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3898855	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4398788	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62467809	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62467857	0.81[AMR][1000 genomes]
rs6460305	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs66525610	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6943696	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6947808	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960778	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6961186	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965056	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6967809	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6968619	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6977632	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71563125	0.82[AMR][1000 genomes]
rs732465	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7357230	0.81[AFR][1000 genomes]
rs801190	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs801191	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801193	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs801196	0.81[AMR][1000 genomes]
rs801207	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	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
9	nsv970868	chr7:66035219-66056610	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4718378	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs4718378	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs4718378	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4718378	RP4-756H11.3	cis	Thyroid	GTEx
rs4718378	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs4718378	RP4-756H11.3	cis	lung	GTEx
rs4718378	RP4-756H11.3	cis	Artery Aorta	GTEx
rs4718378	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4718378	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs4718378	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs4718378	RP4-756H11.3	cis	Artery Tibial	GTEx
rs4718378	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs4718378	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs4718378	GTF2IRD1P1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66021800-66056400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:66023200-66049800	Weak transcription	Stomach Mucosa	stomach
5	chr7:66023200-66055400	Weak transcription	Fetal Brain Male	brain
6	chr7:66024200-66051200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:66024200-66055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:66024200-66055600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:66024400-66051600	Weak transcription	Spleen	Spleen
10	chr7:66037600-66056400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:66037800-66051200	Weak transcription	Small Intestine	intestine
12	chr7:66037800-66054800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:66038000-66052400	Weak transcription	Psoas Muscle	Psoas
14	chr7:66038000-66056200	Weak transcription	Colonic Mucosa	Colon
15	chr7:66038200-66055400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr7:66038200-66055800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:66038400-66055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:66038800-66055400	Weak transcription	Fetal Lung	lung
19	chr7:66039200-66054600	Weak transcription	Fetal Brain Female	brain
20	chr7:66039400-66051200	Weak transcription	Ovary	ovary
21	chr7:66039400-66054200	Weak transcription	Right Ventricle	heart
22	chr7:66039400-66054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:66039400-66055400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:66039400-66055400	Weak transcription	Fetal Kidney	kidney
25	chr7:66039400-66055400	Weak transcription	HUVEC	blood vessel
26	chr7:66039400-66055400	Weak transcription	NH-A	brain
27	chr7:66039600-66054800	Weak transcription	Esophagus	oesophagus
28	chr7:66039800-66055400	Weak transcription	HSMMtube	muscle
29	chr7:66040000-66051600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:66040200-66056200	Weak transcription	Aorta	Aorta
31	chr7:66040400-66051600	Weak transcription	Lung	lung
32	chr7:66041400-66051800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr7:66042000-66054600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:66042000-66054600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:66042000-66055800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:66042200-66053800	Weak transcription	Hela-S3	cervix
37	chr7:66042200-66055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:66042600-66050200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:66043000-66052400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr7:66043000-66055400	Weak transcription	GM12878-XiMat	blood
41	chr7:66044000-66050000	Strong transcription	Fetal Stomach	stomach
42	chr7:66044000-66051000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:66044400-66051200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:66044600-66050200	Strong transcription	NHEK	skin
45	chr7:66044600-66052600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:66045000-66052400	Weak transcription	Right Atrium	heart
47	chr7:66045000-66055200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:66045200-66055800	Weak transcription	Brain Angular Gyrus	brain
49	chr7:66046000-66050000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:66046000-66050200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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