Variant report

Variant	rs12622708
Chromosome Location	chr2:54735006-54735007
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165641	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1112919	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12463484	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12475598	0.81[EUR][1000 genomes]
rs12477376	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13387476	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17045941	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4283459	0.82[EUR][1000 genomes]
rs4519565	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4567979	0.86[EUR][1000 genomes]
rs4671223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671224	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4671227	0.85[EUR][1000 genomes]
rs4671952	0.88[EUR][1000 genomes]
rs4671959	0.85[EUR][1000 genomes]
rs4671962	0.83[EUR][1000 genomes]
rs60294349	0.80[EUR][1000 genomes]
rs6545428	0.89[EUR][1000 genomes]
rs6545433	0.82[EUR][1000 genomes]
rs6717713	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6717816	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739099	0.83[EUR][1000 genomes]
rs68134840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309255	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12622708	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54712400-54737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
3	chr2:54725200-54737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
6	chr2:54727600-54737800	Weak transcription	A549	lung
7	chr2:54728000-54737400	Weak transcription	HSMM	muscle
8	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
9	chr2:54730200-54735400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:54730200-54736800	Weak transcription	Placenta	Placenta
11	chr2:54730400-54736800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:54730600-54735600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:54730600-54736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
17	chr2:54730600-54739400	Weak transcription	HepG2	liver
18	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:54730800-54736800	Weak transcription	Fetal Brain Male	brain
20	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
21	chr2:54731200-54737400	Weak transcription	Fetal Stomach	stomach
22	chr2:54731400-54736200	Weak transcription	Psoas Muscle	Psoas
23	chr2:54731400-54736600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:54731600-54735800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:54731800-54735200	Weak transcription	Right Atrium	heart
26	chr2:54732400-54736600	Weak transcription	HSMMtube	muscle
27	chr2:54732400-54737400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:54732600-54735400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:54732600-54737400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:54732600-54738200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:54732800-54735600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:54732800-54735600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:54732800-54735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:54732800-54735800	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:54732800-54735800	Weak transcription	Brain Substantia Nigra	brain
36	chr2:54732800-54736800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:54732800-54736800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:54732800-54736800	Weak transcription	Liver	Liver
39	chr2:54732800-54736800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:54732800-54736800	Weak transcription	NHDF-Ad	bronchial
41	chr2:54732800-54737400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:54732800-54737400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:54732800-54737600	Weak transcription	NHLF	lung
44	chr2:54732800-54740000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
46	chr2:54733000-54735400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:54733000-54735600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:54733000-54735600	Weak transcription	Adipose Nuclei	Adipose
49	chr2:54733000-54735600	Weak transcription	Brain Angular Gyrus	brain
50	chr2:54733000-54735800	Weak transcription	Fetal Muscle Leg	muscle

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