Variant report

Variant	rs12479
Chromosome Location	chr21:15745269-15745270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15743793..15747020-chr21:15754018..15757060,4	K562	blood:
2	chr21:15738341..15740358-chr21:15745168..15748188,3	MCF-7	breast:
3	chr21:15733160..15735734-chr21:15743714..15745323,2	K562	blood:
4	chr21:15738717..15742131-chr21:15743462..15746963,4	K562	blood:

Variant related genes	Relation type
ENSG00000155304	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1040330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13048179	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13048477	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037941	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2142240	0.81[AMR][1000 genomes]
rs2822624	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2822629	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2822631	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822632	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2822638	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2822644	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2822649	0.83[JPT][hapmap]
rs2822650	0.83[JPT][hapmap]
rs2822652	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2822655	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2822661	0.83[JPT][hapmap]
rs2822662	0.86[GIH][hapmap];1.00[JPT][hapmap]
rs7276170	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7282521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9305301	0.88[ASN][1000 genomes]
rs9974630	0.82[ASN][1000 genomes]
rs9982492	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064554	chr21:15676222-15809321	Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1061686	chr21:15724570-15765777	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv913403	chr21:15743387-15786271	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12479	HSPA13	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15734400-15745600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:15734600-15745400	Weak transcription	HUVEC	blood vessel
3	chr21:15734800-15745400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr21:15737400-15745400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr21:15738600-15746000	Weak transcription	Ovary	ovary
6	chr21:15739200-15747800	Weak transcription	Esophagus	oesophagus
7	chr21:15739800-15745600	Weak transcription	GM12878-XiMat	blood
8	chr21:15739800-15746000	Weak transcription	K562	blood
9	chr21:15740400-15746000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr21:15740600-15745400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr21:15740600-15746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr21:15740600-15746000	Weak transcription	NHLF	lung
13	chr21:15740800-15746000	Weak transcription	Left Ventricle	heart
14	chr21:15741000-15745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr21:15741000-15746000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr21:15741000-15746000	Weak transcription	Fetal Muscle Leg	muscle
17	chr21:15741200-15745800	Weak transcription	Brain Hippocampus Middle	brain
18	chr21:15741200-15745800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr21:15741200-15745800	Weak transcription	Thymus	Thymus
20	chr21:15741200-15746000	Weak transcription	Aorta	Aorta
21	chr21:15741200-15746000	Weak transcription	Right Ventricle	heart
22	chr21:15741200-15748000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr21:15741400-15745400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr21:15741400-15745800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr21:15741600-15745800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr21:15741800-15748000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr21:15742400-15745400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr21:15742800-15745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr21:15742800-15745800	Weak transcription	HSMMtube	muscle
30	chr21:15743000-15745600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:15743400-15745600	Weak transcription	Primary T cells from cord blood	blood
32	chr21:15743400-15745600	Weak transcription	NH-A	brain
33	chr21:15743400-15746000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:15743400-15753200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr21:15743600-15745400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr21:15743600-15745800	Weak transcription	A549	lung
37	chr21:15743800-15745400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr21:15743800-15745400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr21:15743800-15745400	Weak transcription	Brain Substantia Nigra	brain
40	chr21:15743800-15745600	Weak transcription	Fetal Lung	lung
41	chr21:15743800-15750600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr21:15743800-15750800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr21:15743800-15752600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:15743800-15754600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr21:15744000-15745600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr21:15744000-15745600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr21:15744000-15745600	Weak transcription	Colon Smooth Muscle	Colon
48	chr21:15744000-15745600	Weak transcription	Fetal Thymus	thymus
49	chr21:15744000-15745600	Weak transcription	Osteobl	bone
50	chr21:15744000-15745800	Weak transcription	Brain Angular Gyrus	brain

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