Variant report

Variant	rs73154895
Chromosome Location	chr7:100137971-100137972
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100127022..100128538-chr7:100137824..100140499,2	MCF-7	breast:
2	chr7:100136348..100138859-chr7:100182557..100185063,3	MCF-7	breast:
3	chr7:100135274..100138223-chr7:100165794..100167927,2	MCF-7	breast:
4	chr7:100025714..100030196-chr7:100134897..100138793,5	K562	blood:
5	chr7:100136576..100139151-chr7:100200299..100204148,3	K562	blood:
6	chr7:100074273..100077650-chr7:100135969..100140252,4	MCF-7	breast:
7	chr7:100073864..100076959-chr7:100134677..100138430,3	K562	blood:

Variant related genes	Relation type
ENSG00000166925	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000242101	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000184414	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]
rs60743967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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	esv3385336	chr7:100134766-100138414	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73154895	LRCH4	cis	Esophagus Muscularis	GTEx
rs73154895	SAP25	cis	Thyroid	GTEx
rs73154895	SAP25	cis	Esophagus Muscularis	GTEx
rs73154895	SAP25	cis	Artery Tibial	GTEx
rs73154895	SAP25	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100136000-100138000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:100136200-100138000	Active TSS	Ovary	ovary
3	chr7:100136200-100139400	Active TSS	Esophagus	oesophagus
4	chr7:100136400-100138000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:100136400-100138000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:100136400-100138000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr7:100136400-100138000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:100136400-100138000	Active TSS	Colonic Mucosa	Colon
9	chr7:100136400-100138000	Active TSS	GM12878-XiMat	blood
10	chr7:100136400-100138200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr7:100136400-100138200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr7:100136400-100138600	Active TSS	HepG2	liver
13	chr7:100136400-100138800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:100136400-100139000	Active TSS	Brain Anterior Caudate	brain
15	chr7:100137000-100138200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr7:100137000-100138200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:100137400-100138000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:100137400-100138000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:100137400-100138000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:100137400-100138000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr7:100137400-100138000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr7:100137400-100138000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:100137400-100138000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:100137400-100138000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:100137400-100138000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr7:100137400-100138000	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr7:100137400-100138000	Flanking Active TSS	Fetal Lung	lung
28	chr7:100137400-100138000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
29	chr7:100137400-100138000	Flanking Active TSS	Right Ventricle	heart
30	chr7:100137400-100138000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr7:100137400-100138000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr7:100137400-100138000	Flanking Active TSS	Osteobl	bone
33	chr7:100137400-100138200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:100137400-100138200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr7:100137400-100138200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr7:100137400-100138200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr7:100137400-100138200	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr7:100137400-100138200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr7:100137400-100138200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:100137400-100138200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:100137400-100138200	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr7:100137400-100138200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr7:100137400-100138200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr7:100137400-100138200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr7:100137400-100138200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr7:100137400-100138200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr7:100137400-100138200	Flanking Active TSS	Thymus	Thymus
48	chr7:100137400-100138200	Flanking Active TSS	Dnd41	blood
49	chr7:100137400-100138200	Flanking Active TSS	Hela-S3	cervix
50	chr7:100137400-100138200	Flanking Active TSS	HUVEC	blood vessel

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