Variant report

Variant	rs12463484
Chromosome Location	chr2:54757604-54757605
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54754602..54758699-chr2:54783105..54787010,4	MCF-7	breast:
2	chr2:54757446..54759466-chr2:54767763..54770756,2	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction
ENSG00000228108	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10165641	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112919	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12467653	0.80[EUR][1000 genomes]
rs12475598	0.82[EUR][1000 genomes]
rs12477376	0.84[EUR][1000 genomes]
rs12622708	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13387476	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4283459	0.83[EUR][1000 genomes]
rs4519565	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4567979	0.87[EUR][1000 genomes]
rs4671223	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671224	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4671227	0.87[EUR][1000 genomes]
rs4671952	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671959	0.86[EUR][1000 genomes]
rs4671962	0.84[EUR][1000 genomes]
rs60294349	0.81[EUR][1000 genomes]
rs6545428	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545433	0.83[EUR][1000 genomes]
rs6739099	0.84[EUR][1000 genomes]
rs68134840	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9309255	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12463484	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
5	chr2:54746600-54758400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:54747000-54760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54747200-54761800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
11	chr2:54750800-54759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:54751000-54759400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:54751000-54759600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:54751000-54760200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:54752000-54760200	Weak transcription	Colonic Mucosa	Colon
17	chr2:54752000-54764600	Weak transcription	Gastric	stomach
18	chr2:54752200-54759600	Weak transcription	Small Intestine	intestine
19	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:54752400-54758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:54752400-54758000	Weak transcription	Aorta	Aorta
23	chr2:54752400-54758000	Weak transcription	NHEK	skin
24	chr2:54752400-54758200	Weak transcription	Fetal Thymus	thymus
25	chr2:54752400-54759600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:54752600-54758000	Weak transcription	HMEC	breast
27	chr2:54752600-54758600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:54752600-54759800	Weak transcription	GM12878-XiMat	blood
29	chr2:54753000-54758800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:54753000-54759000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:54753200-54758000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:54753200-54758200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:54753200-54759800	Strong transcription	Adipose Nuclei	Adipose
34	chr2:54753400-54758600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:54753400-54758800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:54753600-54758600	Strong transcription	Fetal Lung	lung
37	chr2:54753800-54758000	Weak transcription	Right Atrium	heart
38	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:54754000-54760200	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:54754400-54759800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:54754600-54760000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:54754800-54759000	Strong transcription	HSMM	muscle
45	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:54755000-54758800	Weak transcription	Lung	lung
47	chr2:54755000-54761000	Weak transcription	Right Ventricle	heart
48	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:54755200-54759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:54755400-54758600	Weak transcription	Liver	Liver

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