Variant report

Variant	rs13225933
Chromosome Location	chr7:64343118-64343119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 41 )

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

rs_ID	r²[population]
rs10271473	0.81[EUR][1000 genomes]
rs11773228	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11773456	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12532791	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13223142	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13236444	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13236784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830007	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1965558	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1966140	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34238742	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35058955	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35065007	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813700	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829003	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4644117	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4717222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718154	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4718156	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718169	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4718170	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56063644	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62455121	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62458435	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6460199	0.85[CEU][hapmap]
rs6460209	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6953002	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6957266	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6960979	0.80[AMR][1000 genomes]
rs6965861	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7776640	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7777724	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7782713	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7786519	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7796024	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7796284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798063	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7798465	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7805817	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7810293	0.80[CEU][hapmap]
rs7811163	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs867630	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9638209	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1797468	chr7:64296309-64356050	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv1018967	chr7:64318129-64380869	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv21367	chr7:64328624-64345129	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv1818246	chr7:64328632-64344038	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:41)

SNP	Gene	Cis/trans	Tissue	Source
rs13225933	SEPHS1P1	cis	Artery Tibial	GTEx
rs13225933	RP11-797H7.3	cis	Stomach	GTEx
rs13225933	RP11-460N20.4	cis	Adipose Subcutaneous	GTEx
rs13225933	RP11-797H7.5	cis	Thyroid	GTEx
rs13225933	SEPHS1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs13225933	RP11-797H7.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13225933	RP11-797H7.5	cis	Nerve Tibial	GTEx
rs13225933	RP11-667F9.1	cis	Adipose Subcutaneous	GTEx
rs13225933	RP11-797H7.3	cis	Esophagus Mucosa	GTEx
rs13225933	RP11-797H7.5	cis	lung	GTEx
rs13225933	RP11-797H7.3	cis	lung	GTEx
rs13225933	RP11-797H7.5	cis	Artery Tibial	GTEx
rs13225933	SEPHS1P1	cis	Thyroid	GTEx
rs13225933	RP11-797H7.3	cis	Adipose Subcutaneous	GTEx
rs13225933	RP11-797H7.5	cis	Stomach	GTEx
rs13225933	RP11-797H7.5	cis	Esophagus Muscularis	GTEx
rs13225933	RP11-797H7.3	cis	Muscle Skeletal	GTEx
rs13225933	RP11-797H7.5	cis	Skin Sun Exposed Lower leg	GTEx
rs13225933	RP11-797H7.3	cis	Heart Left Ventricle	GTEx
rs13225933	ZNF273	cis	Heart Left Ventricle	GTEx
rs13225933	RP11-460N20.5	cis	Adipose Subcutaneous	GTEx
rs13225933	CCT6P3	cis	Esophagus Mucosa	GTEx
rs13225933	RP11-667F9.1	cis	Nerve Tibial	GTEx
rs13225933	RP11-797H7.5	cis	Heart Left Ventricle	GTEx
rs13225933	CCT6P3	cis	Skin Sun Exposed Lower leg	GTEx
rs13225933	RP11-797H7.3	cis	Artery Tibial	GTEx
rs13225933	RP11-460N20.5	cis	Whole Blood	GTEx
rs13225933	RP11-797H7.3	cis	Artery Aorta	GTEx
rs13225933	INTS4L1	cis	Skin Sun Exposed Lower leg	GTEx
rs13225933	RP11-460N20.5	cis	Thyroid	GTEx
rs13225933	RP11-797H7.3	cis	Thyroid	GTEx
rs13225933	ZNF273	cis	Thyroid	GTEx
rs13225933	RP11-797H7.3	cis	Nerve Tibial	GTEx
rs13225933	SEPHS1P1	cis	Esophagus Muscularis	GTEx
rs13225933	RP11-460N20.5	cis	Nerve Tibial	GTEx
rs13225933	ERV3	cis	multi-tissue	Pritchard
rs13225933	RP11-797H7.3	cis	Whole Blood	GTEx
rs13225933	RP11-797H7.5	cis	Adipose Subcutaneous	GTEx
rs13225933	SEPHS1P1	cis	Nerve Tibial	GTEx
rs13225933	ZNF273	cis	lung	GTEx
rs13225933	RP11-797H7.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64338400-64343800	ZNF genes & repeats	Fetal Brain Female	brain
2	chr7:64341200-64344200	ZNF genes & repeats	Brain Germinal Matrix	brain
3	chr7:64341800-64344000	Active TSS	Colon Smooth Muscle	Colon
4	chr7:64341800-64344800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr7:64342200-64343800	ZNF genes & repeats	Lung	lung
6	chr7:64342200-64343800	ZNF genes & repeats	HSMM	muscle
7	chr7:64342200-64344000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr7:64342400-64343400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
9	chr7:64342400-64343600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:64342400-64344200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:64342400-64344200	Active TSS	Brain Cingulate Gyrus	brain
12	chr7:64342400-64344200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr7:64342400-64344400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:64342400-64344400	Bivalent/Poised TSS	NHEK	skin
15	chr7:64342600-64343200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:64342600-64343200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:64342600-64343200	Bivalent/Poised TSS	Fetal Stomach	stomach
18	chr7:64342600-64343400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:64342600-64343400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:64342600-64343400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
21	chr7:64342600-64343400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:64342600-64343400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
23	chr7:64342600-64343400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr7:64342600-64343400	ZNF genes & repeats	Gastric	stomach
25	chr7:64342600-64343400	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr7:64342600-64343400	Active TSS	NHDF-Ad	bronchial
27	chr7:64342600-64343600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr7:64342600-64343600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr7:64342600-64343600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:64342600-64343600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:64342600-64343600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:64342600-64343600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr7:64342600-64343600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:64342600-64343600	Active TSS	Brain Angular Gyrus	brain
35	chr7:64342600-64343600	Active TSS	Brain Hippocampus Middle	brain
36	chr7:64342600-64343600	Active TSS	Left Ventricle	heart
37	chr7:64342600-64343600	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr7:64342600-64343600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr7:64342600-64343800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:64342600-64343800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:64342600-64343800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr7:64342600-64343800	Active TSS	Aorta	Aorta
43	chr7:64342600-64343800	Active TSS	Brain Anterior Caudate	brain
44	chr7:64342600-64343800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:64342600-64343800	Bivalent/Poised TSS	Colonic Mucosa	Colon
46	chr7:64342600-64343800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr7:64342600-64343800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr7:64342600-64343800	Active TSS	Psoas Muscle	Psoas
49	chr7:64342600-64343800	Active TSS	Right Atrium	heart
50	chr7:64342600-64344000	Active TSS	Brain Inferior Temporal Lobe	brain

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