Variant report

Variant	rs12473338
Chromosome Location	chr2:54838553-54838554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
2	chr2:54829846..54832829-chr2:54836570..54839601,3	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10164713	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1052788	0.89[EUR][1000 genomes]
rs1052820	0.83[EUR][1000 genomes]
rs12467653	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12475342	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475598	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12476489	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12615589	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620195	0.84[AFR][1000 genomes]
rs13387476	0.82[EUR][1000 genomes]
rs17416284	0.86[EUR][1000 genomes]
rs3796012	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817163	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4283459	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4557016	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4567979	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671227	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671959	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671962	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671964	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4671965	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59871921	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60294349	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545433	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6705756	0.86[EUR][1000 genomes]
rs6739099	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67457439	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72618663	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72618664	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9309255	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12473338	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs12473338	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
3	chr2:54827600-54839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54827600-54839200	Weak transcription	Dnd41	blood
5	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54830800-54839200	Weak transcription	Esophagus	oesophagus
7	chr2:54832200-54839200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:54832200-54839200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:54832200-54839200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:54832200-54840800	Weak transcription	K562	blood
11	chr2:54832400-54839200	Weak transcription	Placenta	Placenta
12	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
14	chr2:54832600-54839200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:54832800-54839000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:54832800-54839600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:54833000-54839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:54833000-54839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:54833000-54839400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:54833000-54839600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:54833000-54841000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:54833400-54838800	Weak transcription	Primary B cells from cord blood	blood
23	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
24	chr2:54833600-54839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:54833600-54839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:54833600-54839200	Weak transcription	Psoas Muscle	Psoas
27	chr2:54833600-54839600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:54833600-54840000	Weak transcription	Fetal Kidney	kidney
29	chr2:54833800-54838800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:54833800-54839200	Weak transcription	Thymus	Thymus
31	chr2:54833800-54839200	Weak transcription	NHEK	skin
32	chr2:54833800-54839200	Weak transcription	NHLF	lung
33	chr2:54833800-54840800	Weak transcription	HMEC	breast
34	chr2:54834000-54838600	Weak transcription	GM12878-XiMat	blood
35	chr2:54834000-54838800	Weak transcription	NH-A	brain
36	chr2:54834000-54839000	Weak transcription	Fetal Lung	lung
37	chr2:54834000-54839200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:54834000-54839200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:54834000-54839200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:54834000-54839200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:54834000-54839200	Weak transcription	Fetal Stomach	stomach
42	chr2:54834000-54839200	Weak transcription	HSMM	muscle
43	chr2:54834000-54839400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr2:54834200-54839200	Weak transcription	Fetal Brain Female	brain
45	chr2:54834200-54839400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:54835000-54839200	Enhancers	Liver	Liver
47	chr2:54835400-54839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:54835400-54842600	Enhancers	Fetal Heart	heart
49	chr2:54835600-54839200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:54835800-54838800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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