Variant report

Variant	rs60743967
Chromosome Location	chr7:100141981-100141982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:100024941..100026600-chr7:100141145..100143393,2	K562	blood:
2	chr7:100139938..100142541-chr7:100186760..100189570,2	K562	blood:
3	chr7:100140983..100146932-chr7:100182357..100186194,10	MCF-7	breast:
4	chr7:100141248..100143599-chr7:100200875..100203327,2	K562	blood:
5	chr7:100025997..100028505-chr7:100141449..100143721,2	MCF-7	breast:
6	chr7:100129087..100132540-chr7:100139779..100143432,5	K562	blood:
7	chr7:100026388..100028395-chr7:100140430..100143246,2	MCF-7	breast:
8	chr7:100141487..100144211-chr7:100154594..100158320,3	MCF-7	breast:
9	chr7:100117244..100119280-chr7:100140483..100142893,2	K562	blood:
10	chr7:100079169..100082569-chr7:100139539..100142416,3	K562	blood:
11	chr7:100140502..100142594-chr7:100143525..100145435,2	K562	blood:
12	chr7:100136291..100139067-chr7:100140246..100145508,4	MCF-7	breast:
13	chr7:100098416..100100583-chr7:100140917..100143201,2	MCF-7	breast:
14	chr7:100024941..100027622-chr7:100141781..100145026,4	K562	blood:
15	chr7:100080527..100083060-chr7:100141951..100145813,4	MCF-7	breast:
16	chr7:100129499..100134064-chr7:100138871..100143432,7	K562	blood:
17	chr7:100141735..100143588-chr7:100448245..100450258,2	K562	blood:
18	chr7:100032634..100034621-chr7:100141142..100143252,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224729	Chromatin interaction
ENSG00000266372	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000166924	Chromatin interaction
ENSG00000236305	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000240211	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000106351	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11972116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11977607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978096	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978967	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216707	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406243	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440977	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58509206	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668677	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61309832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318457	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67147615	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67535650	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970240	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154884	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154887	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154891	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154894	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154902	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156207	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156208	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156210	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156211	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711133	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711137	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799695	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
4	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
6	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
7	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
9	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs60743967	SAP25	cis	Artery Tibial	GTEx
rs60743967	LRCH4	cis	Esophagus Muscularis	GTEx
rs60743967	SAP25	cis	Esophagus Muscularis	GTEx
rs60743967	SAP25	cis	Nerve Tibial	GTEx
rs60743967	SAP25	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100137800-100142400	Weak transcription	NHLF	lung
2	chr7:100137800-100142800	Weak transcription	HSMM	muscle
3	chr7:100137800-100143200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:100137800-100143400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:100137800-100144000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr7:100137800-100146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:100138000-100142000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:100138000-100142400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:100138000-100142400	Weak transcription	Fetal Stomach	stomach
10	chr7:100138000-100142600	Weak transcription	NH-A	brain
11	chr7:100138000-100142800	Weak transcription	Fetal Kidney	kidney
12	chr7:100138000-100142800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:100138000-100143000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:100138000-100145400	Weak transcription	Primary B cells from cord blood	blood
15	chr7:100138000-100145400	Weak transcription	Fetal Brain Male	brain
16	chr7:100138000-100145400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr7:100138200-100142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:100138200-100142000	Weak transcription	Placenta	Placenta
19	chr7:100138200-100142000	Weak transcription	Fetal Thymus	thymus
20	chr7:100138200-100142000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:100138200-100142400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:100138200-100142400	Weak transcription	Fetal Lung	lung
23	chr7:100138200-100142400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:100138200-100142400	Weak transcription	HMEC	breast
25	chr7:100138200-100142400	Weak transcription	NHDF-Ad	bronchial
26	chr7:100138200-100142600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:100138200-100142600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:100138200-100142600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:100138200-100142600	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:100138200-100142600	Weak transcription	Thymus	Thymus
31	chr7:100138200-100142800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:100138200-100142800	Weak transcription	Right Ventricle	heart
33	chr7:100138200-100143000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:100138200-100143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:100138200-100143600	Weak transcription	Brain Germinal Matrix	brain
36	chr7:100138200-100146400	Weak transcription	Fetal Brain Female	brain
37	chr7:100138400-100146400	Weak transcription	Dnd41	blood
38	chr7:100139000-100142400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:100139000-100142400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:100139000-100142400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:100139000-100142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:100139200-100144600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:100139800-100143000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr7:100140000-100142400	Enhancers	Hela-S3	cervix
45	chr7:100140000-100142800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:100140000-100144400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:100140000-100145800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr7:100140000-100148000	Enhancers	Primary B cells from peripheral blood	blood
49	chr7:100140400-100142000	Transcr. at gene 5' and 3'	HepG2	liver
50	chr7:100140400-100142800	Enhancers	Muscle Satellite Cultured Cells	--

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