Variant report

Variant	rs73154897
Chromosome Location	chr7:100147506-100147507
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr7:100147429-100148525	GM12878	blood:	n/a	n/a
2	RUNX3	chr7:100147320-100147796	GM12878	blood:	n/a	n/a
3	RUNX3	chr7:100147318-100147781	GM12878	blood:	n/a	n/a
4	EBF1	chr7:100147404-100147801	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:100147230-100147922	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:100147384-100147731	HepG2	liver:	n/a	n/a
7	MTA3	chr7:100147172-100147740	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100145746..100147750-chr7:100180240..100183063,2	K562	blood:
2	chr7:100146512..100148018-chr7:100154524..100156081,2	K562	blood:
3	chr7:100034086..100036624-chr7:100146945..100148605,2	K562	blood:
4	chr7:100076149..100078056-chr7:100145849..100148358,2	MCF-7	breast:

No data

Variant related genes	Relation type
AGFG2	TF binding region
ENSG00000160813	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000166925	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	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11977607	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978967	0.82[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406243	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34440977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307653	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58509206	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668677	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743967	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61309832	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318457	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67147615	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67535650	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970240	1.00[AFR][1000 genomes];1.00[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	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154895	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154902	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156207	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156208	0.93[AFR][1000 genomes];1.00[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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711133	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711136	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711137	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784759	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799695	0.88[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv971157	chr7:100143688-100148402	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73154897	SAP25	cis	Thyroid	GTEx
rs73154897	LRCH4	cis	Esophagus Muscularis	GTEx
rs73154897	SAP25	cis	Nerve Tibial	GTEx
rs73154897	SAP25	cis	Artery Tibial	GTEx
rs73154897	SAP25	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100140000-100148000	Enhancers	Primary B cells from peripheral blood	blood
2	chr7:100142600-100148600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:100144000-100150000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:100144200-100151400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:100144200-100151600	Weak transcription	NHEK	skin
6	chr7:100144200-100167000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:100144400-100147600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:100144400-100153000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:100144400-100154000	Weak transcription	HSMMtube	muscle
10	chr7:100144600-100148000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr7:100144600-100148000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:100144600-100150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:100144600-100150200	Weak transcription	Fetal Kidney	kidney
14	chr7:100144600-100151000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:100144600-100153200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:100144600-100153200	Weak transcription	HMEC	breast
17	chr7:100144800-100147600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr7:100145000-100148400	Genic enhancers	HepG2	liver
19	chr7:100145000-100148600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:100145000-100150800	Weak transcription	Brain Germinal Matrix	brain
21	chr7:100145000-100153200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:100145200-100153200	Weak transcription	Aorta	Aorta
23	chr7:100145200-100167400	Weak transcription	HSMM	muscle
24	chr7:100145400-100151000	Weak transcription	Psoas Muscle	Psoas
25	chr7:100145400-100153200	Weak transcription	NHLF	lung
26	chr7:100145600-100147600	Enhancers	Lung	lung
27	chr7:100145600-100150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:100145600-100157000	Weak transcription	Fetal Brain Male	brain
29	chr7:100145800-100147600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr7:100145800-100148000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:100145800-100148200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:100145800-100148200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:100145800-100149800	Weak transcription	NH-A	brain
34	chr7:100145800-100150000	Weak transcription	Esophagus	oesophagus
35	chr7:100145800-100150000	Weak transcription	Gastric	stomach
36	chr7:100145800-100157600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:100146000-100147600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:100146000-100147600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr7:100146000-100148600	Genic enhancers	Fetal Thymus	thymus
40	chr7:100146000-100150000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:100146000-100151600	Strong transcription	Fetal Intestine Small	intestine
42	chr7:100146200-100148400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr7:100146200-100148400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:100146200-100150200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:100146200-100151400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:100146200-100153800	Weak transcription	NHDF-Ad	bronchial
47	chr7:100146200-100156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:100146200-100165000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr7:100146400-100147800	Strong transcription	Colonic Mucosa	Colon
50	chr7:100146400-100148000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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