Variant report

Variant	rs4283459
Chromosome Location	chr2:54824849-54824850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54823186..54826195-chr2:54832588..54835705,3	K562	blood:
2	chr2:54806062..54808345-chr2:54823269..54826209,2	MCF-7	breast:
3	chr2:54761267..54763626-chr2:54824184..54826863,2	K562	blood:
4	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:
5	chr2:54822853..54825212-chr2:54825239..54827897,2	MCF-7	breast:
6	chr2:54816128..54819257-chr2:54823273..54825897,3	MCF-7	breast:
7	chr2:54824089..54825634-chr2:54854001..54856179,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164713	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10165641	0.85[EUR][1000 genomes]
rs1027950	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs1052788	0.86[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1052820	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1112919	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs12463484	0.83[EUR][1000 genomes]
rs12467653	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12473338	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475342	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12475598	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12476489	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12615589	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12622708	0.82[EUR][1000 genomes]
rs13387476	0.88[EUR][1000 genomes]
rs17416284	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2007020	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs3796012	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817163	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4519565	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs4557016	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4567979	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671223	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4671224	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671227	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671229	0.90[CEU][hapmap]
rs4671952	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs4671959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671964	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4671965	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671966	0.86[AFR][1000 genomes]
rs59871921	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60294349	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545428	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6545433	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6705756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6738725	0.90[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6739099	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67457439	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68134840	0.83[EUR][1000 genomes]
rs72618663	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618664	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309255	0.95[CEU][hapmap];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4283459	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
4	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:54817000-54825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:54817000-54826200	Weak transcription	NHDF-Ad	bronchial
8	chr2:54817400-54825400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:54817600-54825000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:54817600-54825600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:54817800-54825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:54817800-54826200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:54817800-54826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:54818000-54826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:54820800-54826000	Weak transcription	Osteobl	bone
16	chr2:54820800-54826200	Weak transcription	Hela-S3	cervix
17	chr2:54822200-54826200	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:54822200-54827800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr2:54822200-54828800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:54822200-54833800	Genic enhancers	HepG2	liver
21	chr2:54822400-54825200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr2:54822400-54825600	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr2:54822400-54825600	Enhancers	Brain Substantia Nigra	brain
24	chr2:54822400-54825600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:54822400-54825800	Enhancers	Pancreas	Pancrea
26	chr2:54822400-54826000	Enhancers	Right Ventricle	heart
27	chr2:54822400-54826400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:54822400-54827600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:54822400-54827800	Enhancers	Colon Smooth Muscle	Colon
30	chr2:54822400-54833600	Enhancers	Psoas Muscle	Psoas
31	chr2:54822400-54833800	Enhancers	Stomach Mucosa	stomach
32	chr2:54822400-54834000	Enhancers	Right Atrium	heart
33	chr2:54822600-54825000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:54822600-54825000	Enhancers	Spleen	Spleen
35	chr2:54822600-54825200	Enhancers	Esophagus	oesophagus
36	chr2:54822600-54825200	Enhancers	Small Intestine	intestine
37	chr2:54822600-54825800	Enhancers	Brain Angular Gyrus	brain
38	chr2:54822600-54826000	Enhancers	Fetal Thymus	thymus
39	chr2:54822600-54826200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:54822600-54826600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:54822600-54827000	Enhancers	K562	blood
42	chr2:54822600-54827200	Enhancers	Brain Hippocampus Middle	brain
43	chr2:54822800-54825000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr2:54822800-54825200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:54822800-54825400	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr2:54822800-54826200	Enhancers	Left Ventricle	heart
47	chr2:54822800-54827000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:54822800-54831600	Genic enhancers	A549	lung
49	chr2:54823000-54825000	Enhancers	Fetal Lung	lung
50	chr2:54823000-54825200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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