Variant report

Variant	rs11972116
Chromosome Location	chr7:100139831-100139832
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100127022..100128538-chr7:100137824..100140499,2	MCF-7	breast:
2	chr7:100129087..100132540-chr7:100139779..100143432,5	K562	blood:
3	chr7:100079169..100082569-chr7:100139539..100142416,3	K562	blood:
4	chr7:100139020..100140876-chr7:100182345..100184789,2	MCF-7	breast:
5	chr7:100074273..100077650-chr7:100135969..100140252,4	MCF-7	breast:
6	chr7:100129499..100134064-chr7:100138871..100143432,7	K562	blood:
7	chr7:100138658..100141375-chr7:100181990..100184983,5	K562	blood:
8	chr7:100139117..100141375-chr7:100182213..100184983,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166924	Chromatin interaction
ENSG00000266372	Chromatin interaction
ENSG00000166925	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000242101	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11977607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11978096	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11978967	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12154919	0.89[EUR][1000 genomes]
rs12216707	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2406243	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34440977	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56307653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58509206	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60668677	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60743967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61309832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61318457	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67147615	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67535650	0.92[EUR][1000 genomes]
rs6970240	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73154884	0.90[EUR][1000 genomes]
rs73154887	0.90[EUR][1000 genomes]
rs73154891	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73154894	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73154895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73154897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73154902	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73156207	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73156208	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73156210	0.94[EUR][1000 genomes]
rs73156211	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73711133	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73711136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73711137	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7784759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7799695	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11972116	SAP25	cis	Nerve Tibial	GTEx
rs11972116	LRCH4	cis	Esophagus Muscularis	GTEx
rs11972116	SAP25	cis	Thyroid	GTEx
rs11972116	SAP25	cis	Artery Tibial	GTEx
rs11972116	SAP25	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100137400-100140400	Flanking Active TSS	Liver	Liver
2	chr7:100137600-100140200	Weak transcription	Gastric	stomach
3	chr7:100137800-100141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:100137800-100141800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:100137800-100141800	Weak transcription	Left Ventricle	heart
6	chr7:100137800-100141800	Weak transcription	Lung	lung
7	chr7:100137800-100142400	Weak transcription	NHLF	lung
8	chr7:100137800-100142800	Weak transcription	HSMM	muscle
9	chr7:100137800-100143200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:100137800-100143400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:100137800-100144000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr7:100137800-100146600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:100138000-100141600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:100138000-100141600	Weak transcription	Aorta	Aorta
15	chr7:100138000-100141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:100138000-100141800	Weak transcription	Psoas Muscle	Psoas
17	chr7:100138000-100142000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:100138000-100142400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:100138000-100142400	Weak transcription	Fetal Stomach	stomach
20	chr7:100138000-100142600	Weak transcription	NH-A	brain
21	chr7:100138000-100142800	Weak transcription	Fetal Kidney	kidney
22	chr7:100138000-100142800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:100138000-100143000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:100138000-100145400	Weak transcription	Primary B cells from cord blood	blood
25	chr7:100138000-100145400	Weak transcription	Fetal Brain Male	brain
26	chr7:100138000-100145400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr7:100138200-100140000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:100138200-100140000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr7:100138200-100140000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:100138200-100140200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:100138200-100140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:100138200-100140400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:100138200-100140400	Enhancers	Fetal Intestine Small	intestine
34	chr7:100138200-100140800	Weak transcription	Colonic Mucosa	Colon
35	chr7:100138200-100141000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:100138200-100141000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:100138200-100141000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:100138200-100141000	Weak transcription	Osteobl	bone
39	chr7:100138200-100141200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:100138200-100141400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr7:100138200-100141600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr7:100138200-100141600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr7:100138200-100141600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:100138200-100141600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:100138200-100141600	Weak transcription	Fetal Heart	heart
46	chr7:100138200-100141600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:100138200-100141600	Weak transcription	HUVEC	blood vessel
48	chr7:100138200-100141800	Weak transcription	Adipose Nuclei	Adipose
49	chr7:100138200-100141800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:100138200-100141800	Weak transcription	Fetal Muscle Leg	muscle

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