Variant report

Variant	rs7578287
Chromosome Location	chr2:54711229-54711230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs4429513	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4557020	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4599153	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4640425	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4671936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671937	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671938	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671939	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671942	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545410	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6759618	0.93[ASN][1000 genomes]
rs7592594	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7605221	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][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	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7578287	SPTBN1	cis	Muscle Skeletal	GTEx
rs7578287	AC093110.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54701600-54715400	Weak transcription	Fetal Kidney	kidney
2	chr2:54702200-54712200	Enhancers	Fetal Heart	heart
3	chr2:54702400-54712000	Enhancers	Colon Smooth Muscle	Colon
4	chr2:54705200-54712400	Enhancers	Brain Hippocampus Middle	brain
5	chr2:54706800-54711600	Enhancers	HSMMtube	muscle
6	chr2:54707200-54711400	Enhancers	Ovary	ovary
7	chr2:54707200-54712000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:54707200-54712200	Enhancers	Brain Cingulate Gyrus	brain
9	chr2:54707200-54712400	Enhancers	Brain Substantia Nigra	brain
10	chr2:54707600-54717600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:54707800-54712000	Enhancers	Psoas Muscle	Psoas
12	chr2:54707800-54720800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:54708000-54712400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:54708200-54711800	Weak transcription	Stomach Mucosa	stomach
15	chr2:54708800-54712000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:54708800-54712000	Genic enhancers	Fetal Lung	lung
17	chr2:54709000-54711400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:54709000-54712200	Enhancers	Brain Anterior Caudate	brain
19	chr2:54709000-54712400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:54709200-54711800	Enhancers	Spleen	Spleen
21	chr2:54709200-54712000	Enhancers	Right Ventricle	heart
22	chr2:54709600-54711400	Enhancers	Lung	lung
23	chr2:54709600-54711800	Enhancers	HMEC	breast
24	chr2:54709600-54712000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:54709600-54712000	Enhancers	HUVEC	blood vessel
26	chr2:54709600-54712600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:54709800-54711400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:54710000-54711400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:54710000-54711400	Enhancers	Pancreas	Pancrea
30	chr2:54710000-54711400	Enhancers	NHEK	skin
31	chr2:54710000-54711600	Enhancers	Fetal Muscle Trunk	muscle
32	chr2:54710000-54711800	Enhancers	Small Intestine	intestine
33	chr2:54710200-54712000	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:54710200-54712400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:54710400-54711400	Genic enhancers	Left Ventricle	heart
36	chr2:54710400-54711400	Enhancers	HepG2	liver
37	chr2:54710400-54712000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:54710400-54712000	Genic enhancers	Fetal Muscle Leg	muscle
39	chr2:54710600-54711400	Weak transcription	Fetal Brain Male	brain
40	chr2:54710600-54711800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr2:54710600-54711800	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:54710600-54712000	Enhancers	Adipose Nuclei	Adipose
43	chr2:54710600-54725000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:54710800-54711400	Weak transcription	Fetal Brain Female	brain
45	chr2:54710800-54711800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:54710800-54711800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:54710800-54711800	Enhancers	Stomach Smooth Muscle	stomach
48	chr2:54710800-54711800	Enhancers	NHLF	lung
49	chr2:54710800-54712000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:54710800-54712000	Enhancers	Right Atrium	heart

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