Variant report

Variant	rs11211334
Chromosome Location	chr1:47121419-47121420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47120180..47123031-chr1:47124128..47126254,2	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction

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

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

rs_ID	r²[population]
rs10890409	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890413	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211339	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211340	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211351	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1139759	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12026027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs12029031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12038572	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12048954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118483	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138338	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12142631	0.82[EUR][1000 genomes]
rs12733214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440484	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007344	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083486	0.85[JPT][hapmap]
rs2218190	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737729	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660950	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4660957	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs620913	0.92[JPT][hapmap]

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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	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
rs11211334	ATPAF1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
6	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
7	chr1:47108200-47123400	Weak transcription	K562	blood
8	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
9	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
10	chr1:47109600-47123400	Weak transcription	NH-A	brain
11	chr1:47109600-47132600	Weak transcription	HMEC	breast
12	chr1:47109800-47123200	Weak transcription	HepG2	liver
13	chr1:47112200-47125600	Strong transcription	Liver	Liver
14	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:47112800-47125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:47112800-47125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:47113000-47124400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:47113600-47121800	Weak transcription	NHEK	skin
19	chr1:47114600-47124600	Strong transcription	Fetal Thymus	thymus
20	chr1:47115000-47125200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:47115000-47125400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:47115400-47124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:47115800-47121600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:47115800-47121800	Weak transcription	Psoas Muscle	Psoas
26	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
27	chr1:47116000-47121600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:47116000-47121800	Weak transcription	Right Ventricle	heart
29	chr1:47116000-47123800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
31	chr1:47116000-47130000	Weak transcription	Lung	lung
32	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
33	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
34	chr1:47116200-47121600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:47116400-47121800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:47116600-47122200	Weak transcription	HSMMtube	muscle
37	chr1:47116600-47123200	Weak transcription	HSMM	muscle
38	chr1:47116600-47130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:47117000-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:47117400-47121600	Strong transcription	Adipose Nuclei	Adipose
42	chr1:47117600-47124000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:47117600-47124400	Strong transcription	Brain Angular Gyrus	brain
44	chr1:47117600-47125200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:47117600-47125400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:47117600-47125400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:47117600-47125600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:47117600-47125600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:47117600-47125600	Strong transcription	Placenta	Placenta
50	chr1:47117600-47125800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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